RetrogeneDB ID: retro_itri_530

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393298.1:17223189..17224653(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATP6V1A
• Ensembl ID: ENSSTOG00000009445
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A [Source:HGNC Symbol;Acc:851]

Sequence

>retro_itri_530
ATGGATTTCTCCAAGCTACCCAAAATAATCGATGAAGATAAAGAAAGCACATTTGGTTATGTTCATGGGGTCTCAGGGCC
TGTGGTTACAGCCTGTGACATGGCAGGTGCAGCCATGTATGAGCTGGTAAGAGTGGGTCACAGTGAGTTGGTTGGAGAGA
TTATTTGATTGGAAGGTGACATGGCTACTATTCAGGTGTATGAAGAAACTTCTGGTGTATCTGTTGGAGACCCTGTACTC
CGAACTGGAAAACCTCTCTCCGTTGAGCTTGGTCCTGGCATTATGGGAGCCATTTTTGATGGTATTCAAAGACCTTTGTC
AGATATCAGCAGTCAGACCCAAAGTATCTACATCCCCAGAGGAGTAAATGTGTCTGCTCTTAGCAGAGCTGTTAAATGGG
ATTTTACACCATGCAAAAACCTACGGGTTGGTAGCCATATCACTGGTGGAGATATTTATGCAATTGTCAATGAGAACTCA
CTCATCAAACACAAAATCATGTTACCCCCACGAAATGGAGGAACTGTCACTTGTATTGCCCCACCTGGGAATTATGATAC
CTCTGATGTTGTCTTGGAGCTTGAATTTGAAGGTATAAAGGAGAAGTTCAGCGTGGTCCAGGTATGGCCTGTTCGTCAAG
TTCGTCCTGTCACTGAGAAGCTGCCAGCCAATCATCCTTTGCTGACTGGCCAGAGAGTCCTTGGTGCCCTTTTTCTGTGT
GTACAAGGTGGAACTACTGCTATCCCTGGAGCTTTTGGCTGTGGAAAGACGGTGATATCACAGTCTCTCTCCAAGTATTC
CAGTAGTGATGTGATCATTTATGTAGGATGTGGTGAAAGGGGAAACGAGATGTCTGAAGTCCTCCGAGACTTCCCAGAGC
TCACTATGGAAGTTGATGGTAAGGTAGAGTCAATCATGAAGAGGACAGCTTTAGTAGCCAATACCTCCAATATGCCTGTT
GCTGCTGGAGAAGCCTCTATTTATACTGGCATTACACTATCAGAATATTTCCGTGACATGGGCTACCATGTCAGTATGAT
GGCTGACTCTACCTCGAGATGGGCCGAGGCCCTTAGAGAAATCTCAGGTCGCTTAGCTGAAATGCCTGCAGATAGTGGAT
ATCCTGCATATCTTGGTGCACGTCTGGCTTCTTTCTATGAGCGAGCAGGCAGAGTGAAATGTCTTGGAAATCCTGAAAGA
GAAGGAAGTGTCAGCATTGTAGGAGCAGTTTCTCCACCTGGTGGTGATTTTTCTGATCCAGTTACATCTGCTACTCTTGG
TATTGTTCAGGTGTTTTGGGGATTAGATAAGAAACTAGCCCAACGTAAGCATTTCCCCTCTGTCAACTGGCTCATCAGCT
ACAGCAAGTACATGCGTGCATTGGACGAGTACTATGACAAACATTTCACAGAGTTTGTTCCTCTGAGGACCAAAGCTAAG
GAAATTCTTCAGGAAGAAGAAGAC

Alignment

ORF - retro_itri_530 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.95 %
• Parental protein coverage: 79.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDFSKLPKIIDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEET
          MDFSKLPKIIDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEII.LEGDMATIQVYEET
Retrocopy MDFSKLPKIIDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEII*LEGDMATIQVYEET

Parental  SGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDVKWDFTPCKN
          SGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSR.VKWDFTPCKN
Retrocopy SGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRAVKWDFTPCKN

Parental  LRVGSHITGGDIYAIVNENSLIKHKIMLPPRNRGTVTYIAPPGNYDTSDVVLELEFEGIKEKFNMVQVWP
          LRVGSHITGGDIYAIVNENSLIKHKIMLPPRN.GTVT.IAPPGNYDTSDVVLELEFEGIKEKF..VQVWP
Retrocopy LRVGSHITGGDIYAIVNENSLIKHKIMLPPRNGGTVTCIAPPGNYDTSDVVLELEFEGIKEKFSVVQVWP

Parental  VRQVRPVTEKLPANHPLLTGQRVLDALFPCVQGGTTAIPGAFGCGKTVISQSLSKYSNSDVIIYVGCGER
          VRQVRPVTEKLPANHPLLTGQRVL.ALF.CVQGGTTAIPGAFGCGKTVISQSLSKYS.SDVIIYVGCGER
Retrocopy VRQVRPVTEKLPANHPLLTGQRVLGALFLCVQGGTTAIPGAFGCGKTVISQSLSKYSSSDVIIYVGCGER

Parental  GNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAAREASIYTGITLSEYFRDMGYHVSMMADS
          GNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAA.EASIYTGITLSEYFRDMGYHVSMMADS
Retrocopy GNEMSEVLRDFPELTMEVDGKVESIMKRTALVANTSNMPVAAGEASIYTGITLSEYFRDMGYHVSMMADS

Parental  TSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDP
          TSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDP
Retrocopy TSRWAEALREISGRLAEMPADSGYPAYLGARLASFYERAGRVKCLGNPEREGSVSIVGAVSPPGGDFSDP

Parental  VTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEED
          VTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEED
Retrocopy VTSATLGIVQVFWGLDKKLAQRKHFPSVNWLISYSKYMRALDEYYDKHFTEFVPLRTKAKEILQEEED

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_530 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_530 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000020740	1 retrocopy	retro_mmul_150,
Ictidomys tridecemlineatus	ENSSTOG00000009445	1 retrocopy	retro_itri_530 ,