RetrogeneDB ID: retro_pabe_82

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:142815533..142816439(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000015884
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC25A15
• Ensembl ID: ENSPPYG00000005307
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15 [Source:HGNC Symbol;Acc:10985]

Sequence

>retro_pabe_82
ATGAAGTCCAGTCCTGGCATCCAAGCCGCCATCGACCTCACAGCGGGGGCCGCAGGGGGGACAGCGTGTGTACTGACTGG
GCAGCCCTTCGACACAATAAAAGTGAAGATGCAGACGTTCCCTGACCTGTACAAGGGCCTCACCGACTGCTTCCTGAAGA
CATACGCCCAAGTGGGTCTCCGGGGCTTCTACAAGGGCACGGGCCCGGCACTTATGGCCTACGTCGCCGAAAACTCGGTC
CTCTTCATGTGCTACGGGTTCTGCCAGCAGTTTGTCAGGAAAGTGGCTGGAATGGACAAGCAGGCAAAGCTGAGTGATCT
CCAGACTGCAGCCGCGGGGTCCTTCGCCTCTGCATTTGCTGCACTGGCTCTCTGCCCCACTGAGCTTGTGAAGTGCCGGC
TACAGACCATGTATGAAATGGAGATGTCAGGGAAGATAGCAAAAGGCCATAATACAATTTGGTCTGTCGTGAAGGGTATC
CTTAAAAAGGATGGCCCCTTGGGCTTCTACCATGGACTCTCGAGTACTCTACTTCAAGAAGTACCGGGTTATTTCTTTTT
CTTTGGTGGCTATGAACTGAGCCGATCGTTTTTTGCGTCAGGGAGATCAAAAGATGAACTAGGCCCTGTCCATTTGATGT
TAAGTGGTGGAGTTGCTGGAATTTGCCTCTGGCTTGTCGTGTTCCCAGTGGATTGTATTAAATCCAGAATTCAAGTTCTT
TCCATGTATGGGAAACAAGCAGGATTTATTGGTACCCTCTTAAGTGTTGTGAGAAATGAAGGAATAGTAGCCTTATATTC
TGGACTGAAAGCTACTATGATTCGAGCAATCCCTGCCAATGGGGCACTGTTTGTGGCCTATGAATACAGCAGGAAGAGGA
TGATGAGCCAGTTGGAAGCATACTGA

Alignment

ORF - retro_pabe_82 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDVYRGLTDCCLKTYSQVGFRGFYKGTSPA
          MKS.P.IQAAIDLTAGAAGGTACVLTGQPFDT.KVKMQTFPD.Y.GLTDC.LKTY.QVG.RGFYKGT.PA
Retrocopy MKSSPGIQAAIDLTAGAAGGTACVLTGQPFDTIKVKMQTFPDLYKGLTDCFLKTYAQVGLRGFYKGTGPA

Parental  LIANIAENSVLFMCYGFCQQVVRKVAGLDKQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQTMYEM
          L.A..AENSVLFMCYGFCQQ.VRKVAG.DKQAKLSDLQ.AAAGSFASAFAAL.LCPTELVKCRLQTMYEM
Retrocopy LMAYVAENSVLFMCYGFCQQFVRKVAGMDKQAKLSDLQTAAAGSFASAFAALALCPTELVKCRLQTMYEM

Parental  ETSGKIAKSQNTVWSVIKSILRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPV
          E.SGKIAK..NT.WSV.K.IL.KDGPLGFYHGLSSTLL.EVPGYFFFFGGYELSRSFFASGRSKDELGPV
Retrocopy EMSGKIAKGHNTIWSVVKGILKKDGPLGFYHGLSSTLLQEVPGYFFFFGGYELSRSFFASGRSKDELGPV

Parental  PLMLSGGVGGICLWLAVYPVDCIKSRIQVLSMSGKQAGFIRTFINVVKNEGITALYSGLKPTMIRAFPAN
          .LMLSGGV.GICLWL.V.PVDCIKSRIQVLSM.GKQAGFI.T...VV.NEGI.ALYSGLK.TMIRA.PAN
Retrocopy HLMLSGGVAGICLWLVVFPVDCIKSRIQVLSMYGKQAGFIGTLLSVVRNEGIVALYSGLKATMIRAIPAN

Parental  GALFLAYEYSRKLMMNQLEAY
          GALF.AYEYSRK.MM.QLEAY
Retrocopy GALFVAYEYSRKRMMSQLEAY

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	3.87 RPM
SRP007412_cerebellum	0.12 RPM	3.04 RPM
SRP007412_heart	0.00 RPM	1.29 RPM
SRP007412_kidney	0.00 RPM	2.68 RPM
SRP007412_liver	0.00 RPM	38.19 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_82 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_82 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_82 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_44
Pan troglodytes	retro_ptro_2303
Gorilla gorilla	retro_ggor_2294

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017797	1 retrocopy	retro_cjac_1776,
Cavia porcellus	ENSCPOG00000005570	2 retrocopies	retro_cpor_105, retro_cpor_107,
Equus caballus	ENSECAG00000007666	1 retrocopy	retro_ecab_72,
Homo sapiens	ENSG00000102743	1 retrocopy	retro_hsap_44,
Gorilla gorilla	ENSGGOG00000025261	1 retrocopy	retro_ggor_2294,
Microcebus murinus	ENSMICG00000007218	1 retrocopy	retro_mmur_18,
Macaca mulatta	ENSMMUG00000022585	1 retrocopy	retro_mmul_199,
Nomascus leucogenys	ENSNLEG00000001185	1 retrocopy	retro_nleu_1704,
Otolemur garnettii	ENSOGAG00000009380	1 retrocopy	retro_ogar_490,
Pongo abelii	ENSPPYG00000005307	1 retrocopy	retro_pabe_82 ,
Pan troglodytes	ENSPTRG00000005809	1 retrocopy	retro_ptro_2303,
Pteropus vampyrus	ENSPVAG00000010393	1 retrocopy	retro_pvam_15,
Ictidomys tridecemlineatus	ENSSTOG00000007840	1 retrocopy	retro_itri_726,
Tupaia belangeri	ENSTBEG00000017239	1 retrocopy	retro_tbel_4583,