RetrogeneDB ID: retro_pabe_3805

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:114993042..114994552(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: API5
• Ensembl ID: ENSPPYG00000003345
• Aliases: None
• Description: apoptosis inhibitor 5 [Source:RefSeq peptide;Acc:NP_001126616]

Sequence

>retro_pabe_3805
CAGCATAAAAATGCCTATGAAGTGATACTGGGTGGTGTGAAAGGTAGTATTAAGGAAAAACGATTAGCAGCTCAATTTAT
TCCGAAATTCTTTAAGCATCTTCCAGAATTGGCTGATTCTGTTATCAATACACAGTTAGACCTCTGTGAGGATGAAGATG
TATCTATTCGACCTCAAGCAATTAAAGAACTGCCTCAATTTGCCACTGGAGAAAATCTTCCTCGAGTGGCAGATATACTA
ATGCAACTTCTGCAGACAGATGACTCTGCAGAATTTAACCTAGTGAACAATGCCCTGTTAAGTATATTTAAAATGGATGC
AAAAGGGACTTTAGGTGGGTTGTTCAGCCAAATACTTCAAGGAGAGGACATTGTTAGAGAACGAGCAATTAAATTCCTTT
CTACAAAACTTAAGAGTTTACCAGATGAAGTCTTAACAAAGGAAGTGAAAAGAGCTTATACTAACTGAATCCAAAAAGGT
CCTAGAAGATGTAACTGGTGAAGAATTTGTTCTATTATGAAGATACTGTCTGGGTTAAAAAGCTTACAAACAGTGAGTGG
AAGATAGCAACTTGTAGAGTTCATGGCTGAACAGGCCGACCTGGAACAGACCTTCAATCCCGCGGATCCTGACTGTGTGT
ACAGGTTCTTACAGTGCACTTGGCAGGCAGTACCCATCTTCTCTAGAATTATCCATTCCACAAGGTTTGTGACATATTTC
TGTGAGCAGATTCTCCCTAAACTCAGTACCTTGACTACCCCAGTGGAAGGTCTTGATATACAGTTGGAGGTATTGAAATT
GTTGGCGGAGATGAGTTCATTTTGTGGTGACATGGAAAAACTAGAAAGAAATTTAAGAAAACTATTTGATAAGTTATTGG
AATACATGCTGCTCCCTCCAGAAGAAGCAGAAAATGGAGAGAATGCTGGTAATGAAGAACCCAAGCTACAGTTCAGTTAT
GTGGAATGTTTGTTGTACAGTTTTCACCAGTTGGACTGAAAACATCCAGATTTCTTAACAGCCAAACTGAATGCAAAAAA
GCTCAAAGATTTCAAAATCAGGCTTCAGTACTTTGCACGGGGCCCGCAAGTTTATATCAGACAACTTCGCTTAGCTCTCC
AGGGTAAAACGGGTGAGGCCTTAAAAACAGAAGAGAACAAGATTAAAGTCGTTGCATTGAAAATAACAAAAAATATCAAT
GCTTTAATCAAGGATCTCTTCCACATTCCTCCTTCTTATAAGAGCACAGTAACACTATCCTGGAAACCTGTACAAAAGGT
TGAGATTGGGCAAAAGAGAGCCAGTGAAGATACAACTTCAGGTTCACCACCCGAGAAATCTTCAGCAGAACCAAAAAGAG
ATTCCAGGCAGGTTTATAACCCTCCCAGTGGGAAATATAGCAGCAATTTGAGCAACTTTAATTATGAGAGGAGCCTTCAG
GGGAAGTAGAGGTGGCCAAGGTTGGGGCACACGACGAAATCGAGGAAATCGTAGTCGGGGAAGACTCTAC

Alignment

ORF - retro_pabe_3805 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QHKDAYQVILDGVKGGTKEKRLAAQFIPKFFKHFPELADSAINAQLDLCEDEDVSIRRQAIKELPQFATG
          QHK.AY.VIL.GVKG..KEKRLAAQFIPKFFKH.PELADS.IN.QLDLCEDEDVSIR.QAIKELPQFATG
Retrocopy QHKNAYEVILGGVKGSIKEKRLAAQFIPKFFKHLPELADSVINTQLDLCEDEDVSIRPQAIKELPQFATG

Parental  ENLPRVADILTQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKTL
          ENLPRVADIL.QLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLK.L
Retrocopy ENLPRVADILMQLLQTDDSAEFNLVNNALLSIFKMDAKGTLGGLFSQILQGEDIVRERAIKFLSTKLKSL

Parental  PDEVLTKEVE-ELILTESKKVLEDVTGEEFVLF-MKILSGLKSLQTVSGRQQLVELVAEQADLEQTFNPS
          PDEVLTKEV..ELILTESKKVLEDVTGEEFVL..MKILSGLKSLQTVSGR.QLVE..AEQADLEQTFNP.
Retrocopy PDEVLTKEVK>ELILTESKKVLEDVTGEEFVLL<MKILSGLKSLQTVSGR*QLVEFMAEQADLEQTFNPA

Parental  DPDCVDRLLQCTRQAVPLFSKNVHSTRFVTYFCEQVLPNLGTLTTPVEGLDIQLEVLKLLAEMSSFCGDM
          DPDCV.R.LQCT.QAVP.FS...HSTRFVTYFCEQ.LP.L.TLTTPVEGLDIQLEVLKLLAEMSSFCGDM
Retrocopy DPDCVYRFLQCTWQAVPIFSRIIHSTRFVTYFCEQILPKLSTLTTPVEGLDIQLEVLKLLAEMSSFCGDM

Parental  EKLETNLRKLFDKLLEYMPLPPEEAENGENAGNEEPKLQFSYVECLLYSFHQLGRKLPDFLTAKL-AEKL
          EKLE.NLRKLFDKLLEYM.LPPEEAENGENAGNEEPKLQFSYVECLLYSFHQL..K.PDFLTAKL.A.KL
Retrocopy EKLERNLRKLFDKLLEYMLLPPEEAENGENAGNEEPKLQFSYVECLLYSFHQLD*KHPDFLTAKLNAKKL

Parental  KDFKIRLQYFARGLQVYIRQLRLALQGKTGEALKTEENKIKVVALKITNNINVLIKDLFHIPPSYKSTVT
          KDFKIRLQYFARG.QVYIRQLRLALQGKTGEALKTEENKIKVVALKIT.NIN.LIKDLFHIPPSYKSTVT
Retrocopy KDFKIRLQYFARGPQVYIRQLRLALQGKTGEALKTEENKIKVVALKITKNINALIKDLFHIPPSYKSTVT

Parental  LSWKPVQKVEIGQKRASEDTTSGSP-PKKSSAGPK-MPGRFITLPVGNIAAIWATLIMRGAFRGSRGGRG
          LSWKPVQKVEIGQKRASEDTTSGSP.P.......K..PGRFITLPVGNIAAI.ATLIMRGAFRGSRGG.G
Retrocopy LSWKPVQKVEIGQKRASEDTTSGSP>PRNLQQNQKEIPGRFITLPVGNIAAI*ATLIMRGAFRGSRGGQG

Parental  WGTR---GNRSRGRLY
          WGTR...GNRSRGRLY
Retrocopy WGTRRNRGNRSRGRLY

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	0.11 RPM	43.13 RPM
SRP007412_cerebellum	0.24 RPM	40.37 RPM
SRP007412_heart	0.00 RPM	8.43 RPM
SRP007412_kidney	0.07 RPM	18.13 RPM
SRP007412_liver	0.06 RPM	13.83 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3805 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3805 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3805 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4893
Pan troglodytes	retro_ptro_3261
Gorilla gorilla	retro_ggor_3055

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011993	1 retrocopy	retro_cpor_861,
Myotis lucifugus	ENSMLUG00000013546	1 retrocopy	retro_mluc_245,
Macaca mulatta	ENSMMUG00000008827	1 retrocopy	retro_mmul_947,
Mus musculus	ENSMUSG00000027193	1 retrocopy	retro_mmus_2908,
Pongo abelii	ENSPPYG00000003345	1 retrocopy	retro_pabe_3805 ,
Sorex araneus	ENSSARG00000003480	1 retrocopy	retro_sara_55,
Vicugna pacos	ENSVPAG00000012428	1 retrocopy	retro_vpac_289,