RetrogeneDB ID: retro_pabe_295

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:128159449..128160244(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C5orf15
• Ensembl ID: ENSPPYG00000015780
• Aliases: C5orf15, KCT2
• Description: keratinocyte-associated transmembrane protein 2 precursor [Source:RefSeq peptide;Acc:NP_001126803]

Sequence

>retro_pabe_295
ATGGTTGCTGCTGCCCTGAGGAGGATGAGGGGGCCCGCACAAGCAAAACTACTGCCCAGGTTGGCCATCCAAGCCCTTGC
GGGGCTGGTGCGGCCGCTGGTCTTGGCGCTCCTCCTTGTGTCCGCCGCTCTATCCAGTGTTGTATCATGGACTGATTCAC
TGAGCCAAACTGTACTCAACTCAGATATTTCTACTCCAAATGTGAATGCTTTAACACATGAAAAACAAACCAAATCTTCT
ATTTCCCAAATCAGTACCACCCTCCCTCCCACAATGAGTACTGAGAAAAGTGGAGGAGCATCGGTGGCCCCTCATCCCTC
GCCTACACCTCTGTCTCAAGAGGAAGCTGATAACAACGAAGATACTAGCATAGAGGAGGAGGATCTTCTCACGCTGAACA
GTTCTCCATCCACAGCCAAAGACACTCTGGACAGTGGCAATTATGGAGAACCAGACTATGAGTGGACCACGGGCCACAGG
GATGATGACGAGTCTGATGACACCTTGGAAGAAAACAGTGGTTACATGGAAATTGAACAGTCAGTGAAATCTTTTAAGAT
GCCATCCTCAAATATAGAAGAGGAAGATAGCCATTTCTTTTTTCATCTTATTATTTTTGCTTTTTGCATTGCTATTGTCT
ACATTACATATCACAACAAAAGGAAGATTTTTCTTCTGGTTCAAAGCAGGAAATGGCGTGATGGCCTTTGTTCCAAAACA
GTGGAATACCATTGCCTAGATCAGAATGTTAATGAGGCAATGTCTTCTTTGAAGATTACCAATAATTATATTTTT

Alignment

ORF - retro_pabe_295 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAALKRMRGPAQAKLLPGSAIQALVGLARPLVLALLLVSAALSSVVSRTDSPSPTVLNSHISTPNVNA
          M.AAAL.RMRGPAQAKLLP..AIQAL.GL.RPLVLALLLVSAALSSVVS.TDS.S.TVLNS.ISTPNVNA
Retrocopy MVAAALRRMRGPAQAKLLPRLAIQALAGLVRPLVLALLLVSAALSSVVSWTDSLSQTVLNSDISTPNVNA

Parental  LTHENQTKPSISQISTTLPPTMSTEKSGGASVAPHPSPTPLSQEEADNNEDPSIEEEDLLMLNSSPSTAK
          LTHE.QTK.SISQISTTLPPTMSTEKSGGASVAPHPSPTPLSQEEADNNED.SIEEEDLL.LNSSPSTAK
Retrocopy LTHEKQTKSSISQISTTLPPTMSTEKSGGASVAPHPSPTPLSQEEADNNEDTSIEEEDLLTLNSSPSTAK

Parental  DTLDNGDYGEPDYDWTTGPRDDDESDDTLEENRGYVEIEQSVKSFKMPSSNIEEEDSHFFFHLIIFAFCI
          DTLD.G.YGEPDY.WTTG.RDDDESDDTLEEN.GY.EIEQSVKSFKMPSSNIEEEDSHFFFHLIIFAFCI
Retrocopy DTLDSGNYGEPDYEWTTGHRDDDESDDTLEENSGYMEIEQSVKSFKMPSSNIEEEDSHFFFHLIIFAFCI

Parental  AVVYITYHNKRKIFLLVQSRKWRDGLCSKTVEYHRLDQNVNEAMPSLKITNDYIF
          A.VYITYHNKRKIFLLVQSRKWRDGLCSKTVEYH.LDQNVNEAM.SLKITN.YIF
Retrocopy AIVYITYHNKRKIFLLVQSRKWRDGLCSKTVEYHCLDQNVNEAMSSLKITNNYIF

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.07 RPM
SRP007412_cerebellum	0.12 RPM	15.32 RPM
SRP007412_heart	0.00 RPM	11.74 RPM
SRP007412_kidney	0.00 RPM	17.34 RPM
SRP007412_liver	0.03 RPM	17.57 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_295 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_295 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_416
Pan troglodytes	retro_ptro_324

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000021947	1 retrocopy	retro_ggor_416,
Nomascus leucogenys	ENSNLEG00000008019	1 retrocopy	retro_nleu_1021,
Pongo abelii	ENSPPYG00000015780	1 retrocopy	retro_pabe_295 ,
Pan troglodytes	ENSPTRG00000017234	1 retrocopy	retro_ptro_324,
Pteropus vampyrus	ENSPVAG00000012421	1 retrocopy	retro_pvam_171,