RetrogeneDB ID: retro_ptro_2107

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:166370054..166371054(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS5
• Ensembl ID: ENSPTRG00000012209
• Aliases: None
• Description: Mitochondrial ribosomal protein S5 [Source:UniProtKB/TrEMBL;Acc:K7BHW9]

Sequence

>retro_ptro_2107
ACCGCAGATGAGCTGTGGAAAGGTGTTTTAGCAGAGACTGGTGCCGGAGCAAGAAAAGGAAGAGGCAGCAGAACTAAAAA
GAAGAGAAGAAAGGATTTGAACAGGGGTCAGATCATTGGTGAAGGGCATTATGGTTTCTGTGGCCTGGTCTGAAGGTCTC
TCTTATTAAAAATGGAGCAGTACAGATCATTGCCCAAAAAAGCAAGGAAGAACAGGAGGAGGAGGACAAGATGACCCAGC
AGAGAGAAGAATGGGACCGGAAGAGGAGGATGAAGATAAATGAGAGCGAGGATGCAGTGGAAACTTGTGGGGAGGCATCA
GTCTTAGCCCTCTGACCCTGGTCCCAACAGAGAAACATATGGTAATTTTGATACTAGGATACGTGAGGTAGGAAATGTTT
TCAATAGGACAGCAAAAGAGGGAAGAAAGAGATTGGTAGGTGTCCTGCAGGCTGTGGGGAATGGACAACGAGCTTCAAGT
TTTGCTGTTGTGAAAGCCACTAAATAAATAGATAGATGCTTTCAGAAAAGCAAAGAATAGAGCAATTCACTATTTGCATT
ATATAGAACGATATGAAGACCATACAATATTCCATGATATTTCCTTAAGATTTAAAAGGAGGCATATCAAGATGAAGAAA
CAACCCAGAGGTTACAAGGTCTGCTGCCACAGGGCCATCAACACCATATGCCAGCTCGCTGGCATCAAAGACATGTATGC
CAAGGTCTCTGGGTCCATCAGTATGCTCCCCCTCACCTGGGGCCTCTTCCATGGGCTCTCAGTCAGAAACCTGTCAACAG
CTGGCAGGTAAGAAGGGCCTCCAAGTTGTGGAATTCTGGGAGGAATGTGACCCTCTGCCTATCGTGGTTTCCTCCCCAGG
GGGACCTTGAAAAAGGAGCCAGGTGATGAGGTTCCACATATCAAACTGGACTTAGAAGAAGTGAATGCTCTACAGGGAAT
GTGGTGCTCTGTGCGGTCGGGTTTCTAGAGAGCCGCCACG

Alignment

ORF - retro_ptro_2107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.01 %
• Parental protein coverage: 78.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  TADELWKGALAETGAGAKKGRGKRTKKKKRKDLNRGQIIGEGRYG-FLWPGLNVPLMKNGAVQTIAQRSK
          TADELWKG.LAETGAGA.KGRG.RTKKK.RKDLNRGQIIGEG.YG.FLWPGL.V.L.KNGAVQ.IAQ.SK
Retrocopy TADELWKGVLAETGAGARKGRGSRTKKKRRKDLNRGQIIGEGHYG<FLWPGLKVSLIKNGAVQIIAQKSK

Parental  EEQEKVEADMIQQREEWDRKKKMKV-KRERGWSGNSWGGISLG-PPDPGPCGETYEDFDTRILEVRNVFT
          EEQE..E..M.QQREEWDRK..MK..K.ERG.SGN.WGGISL..P.DPGP..ETY..FDTRI.EV.NVF.
Retrocopy EEQEE-EDKMTQQREEWDRKRRMKI<K*ERGCSGNLWGGISLS<PSDPGPNRETYGNFDTRIREVGNVFN

Parental  MTAKEGRKKSIRVLVAVGNGKGAAGFSIGKATDRMD-AFRK-AKNRAVHHLHYIERYEDHTIFHDISLRF
          .TAKEGRK....VL.AVGNG..A..F...KAT...D..F.K.AKNRA.H.LHYIERYEDHTIFHDISLRF
Retrocopy RTAKEGRKRLVGVLQAVGNGQRASSFAVVKATK*IDRCFQK>AKNRAIHYLHYIERYEDHTIFHDISLRF

Parental  KRTHIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLS-RQTHQQLADKKGL
          KR.HIKMKKQP.GY...CHRAI.TIC.L.GIKDMYAKVSGSI.ML.LT.GLF.GLS...T.QQLA.KKGL
Retrocopy KRRHIKMKKQPRGYKVCCHRAINTICQLAGIKDMYAKVSGSISMLPLTWGLFHGLS>SETCQQLAGKKGL

Parental  HVVEIREECGPLPIVVAS-PRGALRKDPEPEDEVPDVKLDWEDVKTAQGMKRSVWSNLKRAAT
          .VVE..EEC.PLPIVV.S.PRG.L.K..EP.DEVP..KLD.E.V...QGM..SV.S...RAAT
Retrocopy QVVEFWEECDPLPIVVSS<PRGTLKK--EPGDEVPHIKLDLEEVNALQGMWCSVRSGF*RAAT

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	0.07 RPM	27.08 RPM
SRP007412_cerebellum	0.00 RPM	37.17 RPM
SRP007412_heart	0.00 RPM	34.39 RPM
SRP007412_kidney	0.00 RPM	47.81 RPM
SRP007412_liver	0.00 RPM	41.02 RPM
SRP007412_testis	0.00 RPM	24.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2107 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2107 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3116
Gorilla gorilla	retro_ggor_2139
Pongo abelii	retro_pabe_2574
Callithrix jacchus	retro_cjac_2129

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018942	1 retrocopy	retro_cjac_2129,
Homo sapiens	ENSG00000144029	1 retrocopy	retro_hsap_3116,
Gorilla gorilla	ENSGGOG00000001750	1 retrocopy	retro_ggor_2139,
Microcebus murinus	ENSMICG00000007318	1 retrocopy	retro_mmur_565,
Macaca mulatta	ENSMMUG00000016239	2 retrocopies	retro_mmul_2110, retro_mmul_2251,
Mus musculus	ENSMUSG00000027374	1 retrocopy	retro_mmus_2014,
Nomascus leucogenys	ENSNLEG00000000002	1 retrocopy	retro_nleu_1438,
Pongo abelii	ENSPPYG00000012051	1 retrocopy	retro_pabe_2574,
Pan troglodytes	ENSPTRG00000012209	1 retrocopy	retro_ptro_2107 ,