RetrogeneDB ID: retro_pabe_2436

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:63694800..63695280(+)
• Located in intron of: ENSPPYG00000014756

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL22
• Ensembl ID: ENSPPYG00000015979
• Aliases: None
• Description: 39S ribosomal protein L22, mitochondrial [Source:RefSeq peptide;Acc:NP_001126345]

Sequence

>retro_pabe_2436
AGCATTTTACCCCAATCCCACGTCCACACAAGTGGTTCTCTTGACACTTCTCAAAAATGGGAGAAGAAGAATAAAACCAG
TTATCCTCCACAACTGCCTGCAGAACCTCAGAGACCAGCAGAAATCTACCAATACCGAAGAAAACTAAAAGACAGCAAAG
ATAAGATGTTGTATTTGGCAAAATTGGTAGGAGAAATGTCCACTGACCAGGCTTAGCTCAACTGGGATTCAGTGACAAAA
AGGGACCCAAATCATTAAAGAGGTTCTCTTAGAAGCACAAGACGTGGCAGTGAAAGACCACAATGTGGAATTCAGATCCG
GTTTATATATAAACTGAGTCCACCTCAGGGGGAGGCCAGTGCCTGAAAAGTTTCTGCTACCAAAGTAGAAGTTGCTTTGG
GATCATGAAGGTTACTGCCATTATTTTATGAAGCTGGTGGAAGGGCCTCCCCACCTCCATGTGAGGCACCCAAGATGGCG

Alignment

ORF - retro_pabe_2436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.65 %
• Parental protein coverage: 75.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SVLPQSYVHTSASLDISRKWEKKNKIVYPPQLPGEPRRPAEIYHCRRQIKYSKDKMWYLAKLIRGMSIDQ
          S.LPQS.VHTS.SLD.S.KWEKKNK..YPPQLP.EP.RPAEIY..RR..K.SKDKM.YLAKL...MS.DQ
Retrocopy SILPQSHVHTSGSLDTSQKWEKKNKTSYPPQLPAEPQRPAEIYQYRRKLKDSKDKMLYLAKLVGEMSTDQ

Parental  A-LAQLEFNDKKGAK-IIKEVLLEAQDMAVRDHNVEFRSNLYI-AESTSGRGQYLKRIRYHGRGRFGIME
          A.LAQL.F.DKKG.K.IIKEVLLEAQD.AV.DHNVEFRS.LYI..ESTSG.GQ.LK...Y..R..FGIM.
Retrocopy A<LAQLGFSDKKGPK<IIKEVLLEAQDVAVKDHNVEFRSGLYI>TESTSGGGQCLKSFCYQSRSCFGIM-

Parental  KV-YCHYFVKLVEGPP-PPP-EPPKMA
          KV.YCHYF.KLVEGPP.PPP.E.PKMA
Retrocopy KV<YCHYFMKLVEGPP<PPPCEAPKMA

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	17.64 RPM
SRP007412_cerebellum	0.00 RPM	19.58 RPM
SRP007412_heart	0.00 RPM	12.31 RPM
SRP007412_kidney	0.00 RPM	18.86 RPM
SRP007412_liver	0.00 RPM	12.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2436 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2436 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3041
Pan troglodytes	retro_ptro_1997
Gorilla gorilla	retro_ggor_2095
Macaca mulatta	retro_mmul_1889
Callithrix jacchus	retro_cjac_2187

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003875	1 retrocopy	retro_acar_88,
Callithrix jacchus	ENSCJAG00000007325	2 retrocopies	retro_cjac_2187, retro_cjac_2558,
Homo sapiens	ENSG00000082515	1 retrocopy	retro_hsap_3041,
Gorilla gorilla	ENSGGOG00000010232	1 retrocopy	retro_ggor_2095,
Mus musculus	ENSMUSG00000020514	1 retrocopy	retro_mmus_1294,
Nomascus leucogenys	ENSNLEG00000016692	1 retrocopy	retro_nleu_1928,
Pongo abelii	ENSPPYG00000015979	1 retrocopy	retro_pabe_2436 ,
Pan troglodytes	ENSPTRG00000017453	1 retrocopy	retro_ptro_1997,