RetrogeneDB ID: retro_itri_234

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:5224900..5226055(+)
• Located in intron of: ENSSTOG00000000719

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAIP1
• Ensembl ID: ENSSTOG00000011203
• Aliases: None
• Description: poly(A) binding protein interacting protein 1 [Source:HGNC Symbol;Acc:16945]

Sequence

>retro_itri_234
GAACAAAGGAGGCTCCAGAGAGCTCCACCTAGTTCACAGGATAAAATCTCACAGCAGAATTCGGAGTCAGCAATGGCTAA
ACCCTAGATGGTTGTTGGCTCCTGTGTTAATGCTTAACGGTCTGCAAATGCCCCTGAATTTTATCCATCAGGTTATTCTT
CTAATTATACAGAATCCTATGAGGGTGGTTATGAGTATTATCCCATTCTATCGGAATATGCTCAGGACTTTTTTGAATCA
TCTTATAGAGCGGCCTGACAATTTTGAAACTGAAATTGAACAGTTTGCAGAGACCCTGAATGGCTGAATTACAACAGATG
ATGATGCTTTGCAAGAACTTGTGGAACTCATCTACCTACAGGCTACATCTATCCCAAATTTCTCTTATATGGGAGCTCAC
CTGTCTCATCATCTGACAATAAGCCCACACAGTGGCAACTTCCGCCAATTGCTACTTCAAAGATGTCGCACAGAATATGA
AGCTAAAGATTAAGCTGCAAAAGGAGATGAAATGTCTTAATAACGATTTCATGTAATTGTACTCGTTCTGGGACAATCTT
ATCTTAGCTTGGAGATCAAGGGAACAAATGGACAGGTTACAAGAACAGATGTCCTTCAGGTTGGTCTGAGAGAATTGCTG
AATGCCCTCTTCTCTAATCCTATGAGTGACAACTTAATTAGTGCAGTAAAATTACTGAAGTTGACAGGGTCAGTTTTGGA
AGATGCCTGGAAGGAAAAAGGAAAAGACTGATATGGAATAAATTATTCAGAGAATTGAAAATGTTGTCCTAGATGCAAAC
TGCAGCAGAGATGTAAAACAGATGCTCTTGAAGTTTGCAGGACTCTGGCCAAGTAACTGGGGGTAGAGTTCATACAATTT
TAATATACAGAGAAGCATAACATGAAAATGATCTAACTGCTTTATGAATGAACCGACATTTTATACATCTGACGGTGTTC
CTTTCACTGCAGCTGACCCAGATGATCAAGAGAAATGTCAAGAATTACTTGAAAGAGAGGACTTGTTTCCAGATTATGAA
GAAAATGAAACAGATTTTATCAGGGGGTGGTGATCCATAGTTGGATGATATTGATGATGAGATTGAAGAAGCTTATGAAA
ACTTTTATTTGGAATCAGAGTGTAAGCGAAAACAG

Alignment

ORF - retro_itri_234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.1 %
• Parental protein coverage: 81.46 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EQTRPLRAPPSSQDKISQQNSESAMAKPQVVVAPVLMSKLSANAPEFYPSGYSSNYTESYEDGCEDYPTL
          EQ.R..RAPPSSQDKISQQNSESAMAKP..VV........SANAPEFYPSGYSSNYTESYE.G.E.YP.L
Retrocopy EQRRLQRAPPSSQDKISQQNSESAMAKP*MVVGSCVNA*RSANAPEFYPSGYSSNYTESYEGGYEYYPIL

Parental  SEYVQDF-LNHLTEQPGSFETEIEQFAETLNGWVTTDD-ALQELVELIYQQATSIPNFSYMGARLCNYLS
          SEY.QDF.LNHL.E.P..FETEIEQFAETLNG..TTDD.ALQELVELIY.QATSIPNFSYMGA.....LS
Retrocopy SEYAQDF>LNHLIERPDNFETEIEQFAETLNG*ITTDDDALQELVELIYLQATSIPNFSYMGA----HLS

Parental  HHLTISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADIL
          HHLTISP.SGNFRQLLLQRCRTEYE.KD.AAKGDE....RFH..VL.LG..YL.LEIKGTNGQVTR.D.L
Retrocopy HHLTISPHSGNFRQLLLQRCRTEYEAKD*AAKGDEMS**RFHVIVLVLGQSYLSLEIKGTNGQVTRTDVL

Parental  QVGLRELLNALFSNPMDDNLICAVKLLKLTGSVLEDAWKEKGK-TDMEEIIQRIENVVLDANCSRDVKQM
          QVGLRELLNALFSNPM.DNLI.AVKLLKLTGSVLEDAWKEKGK.TDME.IIQRIENVVLDANCSRDVKQM
Retrocopy QVGLRELLNALFSNPMSDNLISAVKLLKLTGSVLEDAWKEKGK>TDME*IIQRIENVVLDANCSRDVKQM

Parental  LLKLVELRSSNW-GRVHATSTYREATPEND-PNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFF
          LLK...L..SNW.GRVH....YREA..END..N.FMNEPTFYTSDGVPFTAADPD.QEK.QELLERED.F
Retrocopy LLKFAGLWPSNW>GRVHTILIYREA*HEND<SNCFMNEPTFYTSDGVPFTAADPDDQEKCQELLEREDLF

Parental  PDYEENGTD-LSGGGDPYLDDIDDEMDPEIEEAYEKFCLESERKRKQ
          PDYEEN.TD.LSGGGDP.LDDIDDE....IEEAYE.F.LESE.KRKQ
Retrocopy PDYEENETD>LSGGGDP*LDDIDDE----IEEAYENFYLESECKRKQ

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_234 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_234 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020376	1 retrocopy	retro_btau_359,
Cavia porcellus	ENSCPOG00000002525	2 retrocopies	retro_cpor_133, retro_cpor_197,
Erinaceus europaeus	ENSEEUG00000009651	1 retrocopy	retro_eeur_304,
Ochotona princeps	ENSOPRG00000000386	2 retrocopies	retro_opri_185, retro_opri_469,
Ictidomys tridecemlineatus	ENSSTOG00000011203	1 retrocopy	retro_itri_234 ,