See the effects of mutations on gene coding sequences (CDS)

An overview of the effects of mutations on amino acids that occur when bases on CDS are changed

procedure

--Get the CDS from the Refseq NM ID by an appropriate method --Translate the acquired CDS into an amino acid sequence --Reflect the mutation on the acquired CDS --Translate the CDS that reflects the displacement into an amino acid sequence

Obtain CDS from Refseq NM ID by an appropriate method

The data of CCDS project will be used to obtain the CDS ID from the Refseq ID.

The CCDS project provides a standard set of human and mouse consensus coding regions.

Download CCDS file

Get CCDS2Sequence.current.txt to find out the CCDS ID from the Refseq ID

curl -LO ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human/CCDS2Sequence.current.txt

The first column of this tab-delimited text is the CCD ID, and the fifth column is the Refseq nucleotide_ID.

#ccds	original_member	current_member	source	nucleotide_ID	protein_ID	status_in_CCDS	sequence_status
CCDS2.2	1	0	NCBI	NM_152486.2	NP_689699.2	Updated	0
CCDS2.2	0	1	NCBI	NM_152486.3	NP_689699.2	Accepted	1
CCDS2.2	1	1	EBI,WTSI	ENST00000342066.7	ENSP00000342313.3	Accepted	1
...(Omitted below)

Obtain the CCDS ID from the Refseq ID

Let's easily find the CCD ID from Refseq ID "NM_130786"

% grep "NM_130786." CCDS2Sequence.current.txt 
CCDS12976.1	1	0	NCBI	NM_130786.3	NP_570602.2	Updated	0
CCDS12976.1	0	1	NCBI	NM_130786.4	NP_570602.2	Accepted	1

From this result, it can be seen that "NM_130768.4" was selected as the consensus for "NM_130768" and "CCDS12976.1" is the corresponding CCDID ID.

Get CDS from CCDS ID

Get CCDS_nucleotide.current.fna.gz to get the CDS

curl -LO ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human/CCDS_nucleotide.current.fna.gz

Recompress the obtained `CCDS_nucleotide.current.fna.gz` file

Since CCDS_nucleotide.current.fna.gz is a fasta format file, it is expanded once to refer to the data using samtools faidx and compressed again using the bgzip command.

Extract the CCDS_nucleotide.current.fna.gz file with gunzip

$ gunzip  CCDS_nucleotide.current.fna.gz

Compress with bgzip and create an index

$ bgzip -i CCDS_nucleotide.current.fna

Since bgzip supports multiple threads, it operates at high speed by specifying a certain number of threads with the option -@ number of threads. Originally, it is compressed for each block, so it may be suitable for speeding up by threads. The result of changing the number of threads as a trial is as follows (up to 8 threads because the execution environment is Quad-Core Intel Core i7)

$ time bgzip -i -@ 1 CCDS_nucleotide.current.fna
bgzip -i -@ 1 CCDS_nucleotide.current.fna  9.58s user 0.08s system 99% cpu 9.739 total
$ gunzip  CCDS_nucleotide.current.fna.gz
$
$time bgzip -i -@ 4 CCDS_nucleotide.current.fna
bgzip -i -@ 4 CCDS_nucleotide.current.fna  10.21s user 0.12s system 391% cpu 2.638 total
$ gunzip  CCDS_nucleotide.current.fna.gz
$
$ time bgzip -i -@ 8 CCDS_nucleotide.current.fna
bgzip -i -@ 8 CCDS_nucleotide.current.fna  11.89s user 0.12s system 710% cpu 1.689 total

Looking at the compression time, it is reduced from 9.6 seconds to 1.7 seconds (since the calculation time is short, there is not much benefit in this example)

Get CDS from CCDS

Header information is needed to get the array from the fasta file Get information for headers that include "CCDS12976.1" Here, the index file for fasta is used.

$ grep 'CCDS12976.1' CCDS_nucleotide.current.fna.gz.fai | cut -f 1
CCDS12976.1|Hs109|chr19

Now that we know the header information, use samtools faidx to get the CDS In the header string|Because it contains, sandwich it with double quotation marks"CCDS12976.1|Hs109|chr19"Search as

$ samtools faidx CCDS_nucleotide.current.fna.gz "CCDS12976.1|Hs109|chr19" 
>CCDS12976.1|Hs109|chr19
ATGTCCATGCTCGTGGTCTTTCTCTTGCTGTGGGGTGTCACCTGGGGCCCAGTGACAGAA
GCAGCCATATTTTATGAGACGCAGCCCAGCCTGTGGGCAGAGTCCGAATCACTGCTGAAA
...(Omission)
GAATCGGAGCTCAGCGACCCTGTGGAGCTCCTGGTGGCAGAAAGCTGA

Nucleotide sequence to amino acid sequence conversion and mutation adaptation

Now that the sequence has been obtained, prepare a program to determine the effect on the amino acid sequence when the mutation is considered to simply change the CDS.

Prepare the tools you need

translate_cds(cds_sequence) --Generate amino acid sequence by inputting cds sequence --STOP is converted to "*"
retrieve_base_sequence_from_fasta(fasta) --Generate an array excluding headers and line breaks from one array of fasta data
compare_sequence(target1, target2, line_length=60): --Compares the input arrays target1 and target2 and outputs the part that is different from the matching part.
apply_snp(sequence, position, ref, alt) --Create an array by replacing ref at the specified position of the given array with ʻalt`
apply_del(sequence, position1, position2) --Create an array with position2 deleted from the specified position position1 of the given array
apply_ins(sequence, position, insertion) --Generate an array with the insertion array inserted at the specified position of the given array

`cds2protein.py`


from math import ceil

def translate_cds(cds_sequence):
    """
    Return translated AA sequence from base sequence.
    """
    translation_table = {
        'AAA': 'K', 'AAC': 'N', 'AAG': 'K', 'AAT': 'N',
        'ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T',
        'AGA': 'R', 'AGC': 'S', 'AGG': 'R', 'AGT': 'S',
        'ATA': 'I', 'ATC': 'I', 'ATG': 'M', 'ATT': 'I',
        'CAA': 'Q', 'CAC': 'H', 'CAG': 'Q', 'CAT': 'H',
        'CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCT': 'P',
        'CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGT': 'R',
        'CTA': 'L', 'CTC': 'L', 'CTG': 'L', 'CTT': 'L',
        'GAA': 'E', 'GAC': 'D', 'GAG': 'E', 'GAT': 'D',
        'GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCT': 'A',
        'GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGT': 'G',
        'GTA': 'V', 'GTC': 'V', 'GTG': 'V', 'GTT': 'V',
        'TAA': '*', 'TAC': 'Y', 'TAG': '*', 'TAT': 'Y',
        'TCA': 'S', 'TCC': 'S', 'TCG': 'S', 'TCT': 'S',
        'TGA': '*', 'TGC': 'C', 'TGG': 'W', 'TGT': 'C',
        'TTA': 'L', 'TTC': 'F', 'TTG': 'L', 'TTT': 'F'
    }
    if len(cds_sequence) < 3:
        return ""

    cds_length = int(len(cds_sequence) / 3)
    return "".join([translation_table[cds_sequence[i * 3:(i + 1) * 3].upper()] for i in range(cds_length)])


def retrieve_base_sequence_from_fasta(fasta):
    """
    Returns continuous sequence without header.
    """
    return "".join([item for item in fasta.splitlines() if not item.startswith(">")])


def compare_sequence(target1, target2, line_length=60):
    """
    Compare sequence and print difference with "X"
    """
    common_length = min(len(target1), len(target2))
    rows = ceil(common_length / line_length)

    difference = ''.join(["." if target1[i] == target2[i] else 'X' for i in range(common_length)])
    for i in range(rows):
        def print_line(sequence):
            print(f"{i * line_length + 1:0=4} {sequence[i * line_length:(i + 1) * line_length]}")

        print_line(target1)
        print_line(difference)
        print_line(target2)
        print()


def apply_snp(sequence, position, ref, alt):
    """
    Return modified sequence at specified position in HGVS.
    """
    if sequence[position - 1] != ref:
        raise ValueError("Base Sequence Mismatch at the specified position.")
    return sequence[0:position - 1] + alt + sequence[position:]


def apply_del(sequence, position1, position2):
    """
    Return modified sequence at specified position in HGVS.
    """
    return sequence[0:position1 - 1] + sequence[position2:]


def apply_ins(sequence, position, insertion):
    """
    Return modified sequence at specified position in HGVS.
    """
    return sequence[0:position] + insertion + sequence[position:]

Let's use this to compare the cds sequence with mutations.

#!/usr/bin/env python
import cds2protein as c2p

# A1BG
fasta_data = '''
>CCDS12976.1|Hs109|chr19
ATGTCCATGCTCGTGGTCTTTCTCTTGCTGTGGGGTGTCACCTGGGGCCCAGTGACAGAA
GCAGCCATATTTTATGAGACGCAGCCCAGCCTGTGGGCAGAGTCCGAATCACTGCTGAAA
CCCTTGGCCAATGTGACGCTGACGTGCCAGGCCCACCTGGAGACTCCAGACTTCCAGCTG
TTCAAGAATGGGGTGGCCCAGGAGCCTGTGCACCTTGACTCACCTGCCATCAAGCACCAG
TTCCTGCTGACGGGTGACACCCAGGGCCGCTACCGCTGCCGCTCGGGCTTGTCCACAGGA
TGGACCCAGCTGAGCAAGCTCCTGGAGCTGACAGGGCCAAAGTCCTTGCCTGCTCCCTGG
CTCTCGATGGCGCCAGTGTCCTGGATCACCCCCGGCCTGAAAACAACAGCAGTGTGCCGA
GGTGTGCTGCGGGGTGTGACTTTTCTGCTGAGGCGGGAGGGCGACCATGAGTTTCTGGAG
GTGCCTGAGGCCCAGGAGGATGTGGAGGCCACCTTTCCAGTCCATCAGCCTGGCAACTAC
AGCTGCAGCTACCGGACCGATGGGGAAGGCGCCCTCTCTGAGCCCAGCGCTACTGTGACC
ATTGAGGAGCTCGCTGCACCACCACCGCCTGTGCTGATGCACCATGGAGAGTCCTCCCAG
GTCCTGCACCCTGGCAACAAGGTGACCCTCACCTGCGTGGCTCCCCTGAGTGGAGTGGAC
TTCCAGCTACGGCGCGGGGAGAAAGAGCTGCTGGTACCCAGGAGCAGCACCAGCCCAGAT
CGCATCTTCTTTCACCTGAACGCGGTGGCCCTGGGGGATGGAGGTCACTACACCTGCCGC
TACCGGCTGCATGACAACCAAAACGGCTGGTCCGGGGACAGCGCGCCGGTCGAGCTGATT
CTGAGCGATGAGACGCTGCCCGCGCCGGAGTTCTCCCCGGAGCCGGAGTCCGGCAGGGCC
TTGCGGCTGCGGTGCCTGGCGCCCCTGGAGGGCGCGCGCTTCGCCCTGGTGCGCGAGGAC
AGGGGCGGGCGCCGCGTGCACCGTTTCCAGAGCCCCGCTGGGACCGAGGCGCTCTTCGAG
CTGCACAACATTTCCGTGGCTGACTCCGCCAACTACAGCTGCGTCTACGTGGACCTGAAG
CCGCCTTTCGGGGGCTCCGCGCCCAGCGAGCGCTTGGAGCTGCACGTGGACGGACCCCCT
CCCAGGCCTCAGCTCCGGGCGACGTGGAGTGGGGCGGTCCTGGCGGGCCGAGATGCCGTC
CTGCGCTGCGAGGGACCCATCCCCGACGTCACCTTCGAGCTGCTGCGCGAGGGCGAGACG
AAGGCCGTGAAGACGGTCCGCACCCCCGGGGCCGCGGCGAACCTCGAGCTGATCTTCGTG
GGGCCCCAGCACGCCGGCAACTACAGGTGCCGCTACCGCTCCTGGGTGCCCCACACCTTC
GAATCGGAGCTCAGCGACCCTGTGGAGCTCCTGGTGGCAGAAAGCTGA
'''

seq2 = c2p.retrieve_base_sequence_from_fasta(fasta_data)
aa_before = c2p.translate_cds(seq2)

# Snp
print()
print("NM_130786.3:c.1481A>T, NM_130786.4:c.1481A>T, NP_570602.2:p.Glu494Val")
seq3 = c2p.apply_snp(seq2, 1481, 'A', 'T')
aa_after = c2p.translate_cds(seq3)
c2p.compare_sequence(aa_before, aa_after)

# Deletion
# rs770249611
print()
print("NM_130786.3:c.1375_1377del, NM_130786.4:c.1375_1377del, NP_570602.2:p.Phe459del")
seq3 = c2p.apply_del(seq2, 1375, 1377)
aa_after = c2p.translate_cds(seq3)
c2p.compare_sequence(aa_before, aa_after)

# rs149623806
print()
print("NM_130786.3:c.66_68del, NM_130786.4:c.66_68del, NP_570602.2:p.Ile23del")
seq3 = c2p.apply_del(seq2, 66, 68)
aa_after = c2p.translate_cds(seq3)
c2p.compare_sequence(aa_before, aa_after)

# rs1454635471
print(
    "NM_130786.3:c.22_23CT[1], NM_130786.4:c.22_23CT[1], NR_015380.2:n.1111_1112GA[1], NR_015380.1:n.1111_1112GA[1], NP_570602.2:p.Leu9fs")
seq3 = c2p.apply_del(seq2, 22, 23)
aa_after = c2p.translate_cds(seq3)
c2p.compare_sequence(aa_before, aa_after)

# rs1290624409
print(
    "NM_130786.4:c.47_56del, NP_570602.2:p.Gly16fs")
seq3 = c2p.apply_del(seq2, 47, 56)
aa_after = c2p.translate_cds(seq3)
c2p.compare_sequence(aa_before, aa_after)

# insertion
# rs1568555027
print(
    "NM_130786.4:c.121_122insA, NP_570602.2:p.Pro41fs")
seq3 = c2p.apply_ins(seq2, 121, "A")
aa_after = c2p.translate_cds(seq3)
c2p.compare_sequence(aa_before, aa_after)

Execution result

NM_130786.3:c.1481A>T, NM_130786.4:c.1481A>T, NP_570602.2:p.Glu494Val

NM_130786.3:c.1481A>T, NM_130786.4:c.1481A>T, NP_570602.2:p.Glu494Val
0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQL
0001 ............................................................
0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQL

0061 FKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPW
0061 ............................................................
0061 FKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPW

0121 LSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNY
0121 ............................................................
0121 LSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNY

0181 SCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVD
0181 ............................................................
0181 SCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVD

0241 FQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELI
0241 ............................................................
0241 FQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELI

0301 LSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFE
0301 ............................................................
0301 LSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFE

0361 LHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAV
0361 ............................................................
0361 LHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAV

0421 LRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTF
0421 ............................................................
0421 LRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTF

0481 ESELSDPVELLVAES*
0481 .............X..
0481 ESELSDPVELLVAVS*

NM_130786.3:c.1375_1377del, NM_130786.4:c.1375_1377del, NP_570602.2:p.Phe459del

0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQL
0001 ............................................................
0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQL

0061 FKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPW
0061 ............................................................
0061 FKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPW

0121 LSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNY
0121 ............................................................
0121 LSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNY

0181 SCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVD
0181 ............................................................
0181 SCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVD

0241 FQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELI
0241 ............................................................
0241 FQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELI

0301 LSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFE
0301 ............................................................
0301 LSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFE

0361 LHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAV
0361 ............................................................
0361 LHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAV

0421 LRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTF
0421 ......................................XXXXXXXXXXXXXXXXXXXXXX
0421 LRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIVGPQHAGNYRCRYRSWVPHTFE

0481 ESELSDPVELLVAES*
0481 XXXXXXXXX.XXXXX
0481 SELSDPVELLVAES*

NM_130786.3:c.66_68del, NM_130786.4:c.66_68del, NP_570602.2:p.Ile23del

0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQL
0001 ......................XXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX
0001 MSMLVVFLLLWGVTWGPVTEAAFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQLF

0061 FKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPW
0061 XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXX
0061 KNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPWL

0121 LSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNY
0121 XXXXXXXXXXXXXX.XXXXXXXXXXXXX.X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX
0121 SMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNYS

0181 SCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVD
0181 XXXXXXXXXXXXXXXXXXXXX.XX.X...XXXX.XXX.XXXXXXXXXXXXXXXXXXXXXX
0181 CSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVDF

0241 FQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELI
0241 XXX.XXXXX.XXXX.XXXXXXX.XXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX
0241 QLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELIL

0301 LSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFE
0301 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.X.XXXXXXXXXXXXXXXX
0301 SDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFEL

0361 LHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAV
0361 XXXXXXXXXXXXXXXXXXXX.XX.XXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX
0361 HNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAVL

0421 LRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTF
0421 XXXXXXXXXXXXX.XXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXX
0421 RCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTFE

0481 ESELSDPVELLVAES*
0481 XXXXXXXXX.XXXXX
0481 SELSDPVELLVAES*

NM_130786.3:c.22_23CT[1], NM_130786.4:c.22_23CT[1], NR_015380.2:n.1111_1112GA[1], NR_015380.1:n.1111_1112GA[1], NP_570602.2:p.Leu9fs

0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQL
0001 ........XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
0001 MSMLVVFLAVGCHLGPSDRSSHIL*DAAQPVGRVRITAETLGQCDADVPGPPGDSRLPAV

0061 FKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPW
0061 XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
0061 QEWGGPGACAP*LTCHQAPVPADG*HPGPLPLPLGLVHRMDPAEQAPGADRAKVLACSLA

0121 LSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNY
0121 .XX.X.XXXXXXXXXXX.X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
0121 LDGASVLDHPRPENNSSVPRCAAGCDFSAEAGGRP*VSGGA*GPGGCGGHLSSPSAWQLQ

0181 SCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVD
0181 XXXXXXX.XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX
0181 LQLPDRWGRRPL*AQRYCDH*GARCTTTACADAPWRVLPGPAPWQQGDPHLRGSPEWSGL

0241 FQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELI
0241 XXXX...XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX.XX.XXXXX
0241 PATARGERAAGTQEQHQPRSHLLSPERGGPGGWRSLHLPLPAA*QPKRLVRGQRAGRADS

0301 LSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFE
0301 XXXXXXX.XXXXXXXXXXXXXXXXXX..XXX.XXXXX.XXXXXX.XXXXXXXXXXX..XX
0301 ER*DAARAGVLPGAGVRQGLAAAVPGAPGGRALRPGARGQGRAPRAPFPEPRWDRGALRA

0361 LHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAV
0361 XXXXXXXXXXXXXXXXXXXXXXX.XX.XXXXXXXXXXX.XXXXXXXXXXX.XXXXX.XXX
0361 AQHFRG*LRQLQLRLRGPEAAFRGLRAQRALGAARGRTPSQASAPGDVEWGGPGGPRCRP

0421 LRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTF
0421 XXXXXXXXXXXXXXX.XXXXXXXXXXXXX.XXXXXXXXXXX.XXXXXXXXXXXXXX..XX
0421 ALRGTHPRRHLRAAARGRDEGREDGPHPRGRGEPRADLRGAPARRQLQVPLPLLGAPHLR

0481 ESELSDPVELLVAES*
0481 XXXXXXXXXXXXXXX
0481 IGAQRPCGAPGGRKL

NM_130786.4:c.47_56del, NP_570602.2:p.Gly16fs

0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQL
0001 ...............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
0001 MSMLVVFLLLWGVTWEKQPYFMRRSPACGQSPNHC*NPWPM*R*RARPTWRLQTSSCSRM

0061 FKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPW
0061 XXXXXXXXXX..X.XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXX.
0061 GWPRSLCTLTHLPSSTSSC*RVTPRAATAAARACPQDGPS*ASSWS*QGQSPCLLPGSRW

0121 LSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNY
0121 XXXXXXXXXXXXXXXXX..X..XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXX
0121 RQCPGSPPA*KQQQCAEVCCGV*LFC*GGRATMSFWRCLRPRRMWRPPFQSISLATTAAA

0181 SCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVD
0181 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX
0181 TGPMGKAPSLSPALL*PLRSSLHHHRLC*CTMESPPRSCTLATR*PSPAWLP*VEWTSSY

0241 FQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELI
0241 XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX.XXXX.XXXXXX
0241 GAGRKSCWYPGAAPAQIASSFT*TRWPWGMEVTTPAATGCMTTKTAGPGTARRSS*F*AM

0301 LSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFE
0301 XXXXXXXX.XXXXXXXXXXXXXX.XXXXXXXXXX.XXXXXXXXXXXXXXXX.XXXXXXXX
0301 RRCPRRSSPRSRSPAGPCGCGAWRPWRARASPWCARTGAGAACTVSRAPLGPRRSSSCTT

0361 LHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAV
0361 XXXXXXXXX.XXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX.X
0361 FPWLTPPTTAASTWT*SRLSGAPRPASAWSCTWTDPLPGLSSGRRGVGRSWRAEMPSCAA

0421 LRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTF
0421 XXXXXXX.XXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX.XXX.XXXXXXXXXXXXXX
0421 RDPSPTSPSSCCARARRRP*RRSAPPGPRRTSS*SSWGPSTPATTGAATAPGCPTPSNRS

0481 ESELSDPVELLVAES*
0481 XXX.XXXXXXXX
0481 SATLWSSWWQKA

NM_130786.4:c.121_122insA, NP_570602.2:p.Pro41fs

0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQL
0001 ........................................X.XXXXXXXXXXXXXXXXXX
0001 MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKHLGQCDADVPGPPGDSRLPA

0061 FKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPW
0061 XXXXXXXXXXXXXXXXXXXXXXXX.XXX.XXXXXX..XXXXXXXXXXXXXXXX.X.XXXX
0061 VQEWGGPGACAP*LTCHQAPVPADG*HPGPLPLPLGLVHRMDPAEQAPGADRAKVLACSL

0121 LSMAPVSWITPGLKTTAVCRGVLRGVTFLLRREGDHEFLEVPEAQEDVEATFPVHQPGNY
0121 XXXXXXXXXX.XXXXXXXXXXXXX.XX.XXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX
0121 ALDGASVLDHPRPENNSSVPRCAAGCDFSAEAGGRP*VSGGA*GPGGCGGHLSSPSAWQL

0181 SCSYRTDGEGALSEPSATVTIEELAAPPPPVLMHHGESSQVLHPGNKVTLTCVAPLSGVD
0181 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX
0181 QLQLPDRWGRRPL*AQRYCDH*GARCTTTACADAPWRVLPGPAPWQQGDPHLRGSPEWSG

0241 FQLRRGEKELLVPRSSTSPDRIFFHLNAVALGDGGHYTCRYRLHDNQNGWSGDSAPVELI
0241 XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX
0241 LPATARGERAAGTQEQHQPRSHLLSPERGGPGGWRSLHLPLPAA*QPKRLVRGQRAGRAD

0301 LSDETLPAPEFSPEPESGRALRLRCLAPLEGARFALVREDRGGRRVHRFQSPAGTEALFE
0301 XXXXXXXXXXXX.XXXXXXX.XXXXXXXXX.XXXXXXXXXX.XXXXXX.XX.XXXXXXXX
0301 SER*DAARAGVLPGAGVRQGLAAAVPGAPGGRALRPGARGQGRAPRAPFPEPRWDRGALR

0361 LHNISVADSANYSCVYVDLKPPFGGSAPSERLELHVDGPPPRPQLRATWSGAVLAGRDAV
0361 XXXXXXXXXXXXXXXXXXXXXX.X.XXXXXX.XXXXXXX.XXXXXXXXXXXXXXX.XXXX
0361 AAQHFRG*LRQLQLRLRGPEAAFRGLRAQRALGAARGRTPSQASAPGDVEWGGPGGPRCR

0421 LRCEGPIPDVTFELLREGETKAVKTVRTPGAAANLELIFVGPQHAGNYRCRYRSWVPHTF
0421 XXXX.XX.XXXXXXXXX.XXXXXXXXXX.XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXX
0421 PALRGTHPRRHLRAAARGRDEGREDGPHPRGRGEPRADLRGAPARRQLQVPLPLLGAPHL

0481 ESELSDPVELLVAES*
0481 XXXXXX.XXXXXXXXX
0481 RIGAQRPCGAPGGRKL

Notes

The amino acid sequence inferred when a mutation is added to cds is just a reference value. It can be used only when the following conditions are met at least

--Mutations are confined to a single exon in cds --Mutations generated in exon do not affect the boundary between exon and intron

I don't know under what conditions the above holds ...

So far this time: smile:

[PYTHON] Obtain the sequence information of the translated protein from the mutation information of CDS