RetrogeneDB ID: retro_ggor_2139

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:173783160..173784160(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS5
• Ensembl ID: ENSGGOG00000001750
• Aliases: None
• Description: None

Sequence

>retro_ggor_2139
ACCGCAGATGAGCTGTGGAAAGCTGTTTTAGCAGAGACTGGTGCTGGAGCAAGAAAAGGAAGAGGCAGCAGAACTAAAAA
GAAGAGAAGAAAGGATTTGAACAGGGGTCAGATCATTGGTGAAGGGCATTATGGTTTCTGTGGCCTGGTCTGAATGTCTC
TCTTATTAAAAATGGAGCAGTACAGATCATTGCCCAAAAAAGCAAGGAAGAACAGAAGGAGGAGGACAACATGACCCAGC
AGAGAGAAGAATGGGACCGGAAGAGGAGGATGAAGATAAATGAGAGCGAGGATGCAGTGGAAACTTGTGGGGAGGCATCA
GTCTTAGCCCTCTGACCCTGGTCCCAACAGAGAAACATATAGTAATTTTGATACCAGGATACTTGAGGTAGGAAATGTTT
TCAATAGGACAGCAAAAGAGGGAAGAAAGAGATTGGTGGGTGTCCTGCAGGCTGTGGGGAATGGACAACGAGCTTCAAGG
TTTGCTGTTGCGAAAGCCACTAAATAAATAGATAGATGCTTTCAGAAAAGCAAAGAATAGAGCAATTCACTATTTGCATT
ATATAGAATGATATGAAGACCATACAATATTCCATGATACTTCATTAAGATTTAAAAGGAGGCATATCAAGATGAAAAAA
CAACCCAGAGTTTACAAGGTCTGCTGCCACAGGGCCATCAACACCATATGCCAGCTCGCTGGCATCAAAGACATGTATGC
CAAGGTCTCTGGGTCCATCAGTATGCTTCCCCTCACCTGGGGCCTCTTCCATGGGCTCTCAGGCAGAAACCCGTCAACAG
CTGGCAGGTAAGAAGGGCCTCCAAGTTGTGGAATTCTGGGAGGAATGTGGCCCTCTGCCTATTGTGGTTGCCTCCCCAGG
GGGACCTTGAAAAAGGAGCCAGGTGATGAGGTTCCACATATCAAACTGGACTTGGAAGAAGTGAATGCTCTACAGGGAAT
GTGGCGCTCTGTGCGGTCGGGTTTCTAGAGAGCCGCCACG

Alignment

ORF - retro_ggor_2139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.17 %
• Parental protein coverage: 78.37 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  TADELWKGALAETGAGAKKGRGKRTKKKKRKDLNRGQIIGEGRYGF-LWPGLNVPLMKNGAVRTIAQRSK
          TADELWK..LAETGAGA.KGRG.RTKKK.RKDLNRGQIIGEG.YGF.LWPGLNV.L.KNGAV..IAQ.SK
Retrocopy TADELWKAVLAETGAGARKGRGSRTKKKRRKDLNRGQIIGEGHYGF<LWPGLNVSLIKNGAVQIIAQKSK

Parental  EEQEKVEADMIQQREEWDRKKKMKV-KRERGWSGNSWGGISLGP-PDPGPCGETYEDFDSRILEVRNVFT
          EEQ.K.E..M.QQREEWDRK..MK..K.ERG.SGN.WGGISL.P..DPGP..ETY..FD.RILEV.NVF.
Retrocopy EEQ-KEEDNMTQQREEWDRKRRMKI<K*ERGCSGNLWGGISLSP<SDPGPNRETYSNFDTRILEVGNVFN

Parental  MTAKEGRKKSIRVLVAVGNGKGAA-GFSIGKATDR-MDAFRKAKNRAVHHLHYIERYEDHTIFHDISLRF
          .TAKEGRK....VL.AVGNG..A..G....K......DAFRKAKNRA.H.LHYIE.YEDHTIFHD.SLRF
Retrocopy RTAKEGRKRLVGVLQAVGNGQRAS>GLLLRKPLNK*IDAFRKAKNRAIHYLHYIE*YEDHTIFHDTSLRF

Parental  KRTHIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSINMLSLTQGLFRGLS-RQ-ETHQQLADKK
          KR.HIKMKKQP..Y...CHRAI.TIC.L.GIKDMYAKVSGSI.ML.LT.GLF.GLS.RQ.ET.QQLA.KK
Retrocopy KRRHIKMKKQPRVYKVCCHRAINTICQLAGIKDMYAKVSGSISMLPLTWGLFHGLS<RQ<ETRQQLAGKK

Parental  GLHVVEIREECGPLPIVVAS-PRGALRKDPEPEDEVPDVKLDWEDVKTAQGMKRSVWSNLKRAAT
          GL.VVE..EECGPLPIVVAS.PRG.L.K..EP.DEVP..KLD.E.V...QGM.RSV.S...RAAT
Retrocopy GLQVVEFWEECGPLPIVVAS<PRGTLKK--EPGDEVPHIKLDLEEVNALQGMWRSVRSGF*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	0.24 RPM	30.16 RPM
SRP007412_cerebellum	0.00 RPM	27.70 RPM
SRP007412_heart	0.00 RPM	21.54 RPM
SRP007412_kidney	0.00 RPM	42.61 RPM
SRP007412_liver	0.00 RPM	33.61 RPM
SRP007412_testis	0.00 RPM	37.71 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2139 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3116
Pan troglodytes	retro_ptro_2107
Pongo abelii	retro_pabe_2574
Callithrix jacchus	retro_cjac_2129

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009757	1 retrocopy	retro_amel_1242,
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,
Myotis lucifugus	ENSMLUG00000003183	1 retrocopy	retro_mluc_2245,
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,