RetrogeneDB ID: retro_chof_762

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_1445:25738..26532(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000012513
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAIP1
• Ensembl ID: ENSCHOG00000004961
• Aliases: None
• Description: poly(A) binding protein interacting protein 1 [Source:HGNC Symbol;Acc:16945]

Sequence

>retro_chof_762
GGGCCTGAGAGCGGCGGTTTCCCGAAAGCAGCGGGGCCTGCTCAGCGGCCCCAGCACCAGCCGCCGCCTCAGCCGAAGCC
CCGGGCTACCTACAGCCGCCGCCGCTGCGCCAGCCCAGAAAGGCCCCGCCGCCCGGGGCCCAGTGCGAGGTCCCCGCCGG
CCCCCAGCGGCCTCCCCAGCCCGGGGCTCTCCCAGAACAAAGAGGTCCTTGAGAGCCCCGCCTAGTTCACAGGATAAAAT
CCCACAGCAGAACTCGGAATCAGCAATTGGCTAAACTCCAGGTGGTTGTAGCTCCTGTATTAATATCTAAGCTGTCTGTG
AGCACCCCGGAATTTTACCCATCAGGTTATTCTTCTAATTATACACAATCCTTCGAGGATGGTTGTGAGGATTATCCTAC
TCTATCAGAATATGTTCAAGACTTTTTGCATCATCTTACAAAGCAACCTGGTCGTTTTGAAACTGAAATTGAACAATTTG
CAGAGACCTTGAATGGCTGGGTTACAACAGATGATGCTTTGCAAGCACTTGAGGAACTCATCTATCAACAGGCTGTATCT
ACCCCAAATTTTTCTTACATGGGAGCTCGCCTTTGTAATTACCTGTCTCATCATCTGACAATTAGCCCACAGAGTGGTAA
CTTCCTCCAATTGCTGCTTCGAAGATGTCGGACTGAATATGAAGTTAAAGATGCAAAAGGGGAAGAAGTGACTCGAAAAC
AATTTCATGCACTTGTCCTCTTTCTAGAACTTCATCTTAACCTGGAGATCAAGGGAACAAATGGACAGGTTACA

Alignment

ORF - retro_chof_762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.5 %
• Parental protein coverage: 55.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GPEGGSLPNGAGPVERPRHQPPPQPK-APGYLQPPPLRQPRTAPPPGAQCEVLTGPQRPPRPGALPEQT-
          GPE.G..P..AGP..RP.HQPPPQPK.APGYLQPPPLRQPR.APPPGAQCEV..GPQRPP.PGALPEQ..
Retrocopy GPESGGFPKAAGPAQRPQHQPPPQPK<APGYLQPPPLRQPRKAPPPGAQCEVPAGPQRPPQPGALPEQR<

Parental  RSLRAPPSSQDKVPQQNSDSA-MAKPQVVVAPVLISKLSVNAPEFYPSGYSSNYTESYEDDCEDYPTLSE
          RSLRAPPSSQDK.PQQNS.SA..AK.QVVVAPVLISKLSV..PEFYPSGYSSNYT.S.ED.CEDYPTLSE
Retrocopy RSLRAPPSSQDKIPQQNSESA>LAKLQVVVAPVLISKLSVSTPEFYPSGYSSNYTQSFEDGCEDYPTLSE

Parental  YVQDFLNHLTEQPGSFETEIEQFAETLNGWVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHLT
          YVQDFL.HLT.QPG.FETEIEQFAETLNGWVTTDDALQ.L.ELIYQQA.S.PNFSYMGARLCNYLSHHLT
Retrocopy YVQDFLHHLTKQPGRFETEIEQFAETLNGWVTTDDALQALEELIYQQAVSTPNFSYMGARLCNYLSHHLT

Parental  ISPQSGNFRQLLLQRCRTEYEVKDQAAKGDEATRKRFHAFVLFLGELYLNLEIKGTNGQVT
          ISPQSGNF.QLLL.RCRTEYEVKD..AKG.E.TRK.FHA.VLFL.EL.LNLEIKGTNGQVT
Retrocopy ISPQSGNFLQLLLRRCRTEYEVKD--AKGEEVTRKQFHALVLFL-ELHLNLEIKGTNGQVT

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_762 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020376	1 retrocopy	retro_btau_359,
Choloepus hoffmanni	ENSCHOG00000004961	1 retrocopy	retro_chof_762 ,
Callithrix jacchus	ENSCJAG00000001340	2 retrocopies	retro_cjac_3224, retro_cjac_3337,
Erinaceus europaeus	ENSEEUG00000009651	1 retrocopy	retro_eeur_304,
Homo sapiens	ENSG00000172239	1 retrocopy	retro_hsap_1726,
Otolemur garnettii	ENSOGAG00000001887	2 retrocopies	retro_ogar_1096, retro_ogar_1241,