RetrogeneDB ID: retro_pabe_2574

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:169605916..169606693(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS5
• Ensembl ID: ENSPPYG00000012051
• Aliases: None
• Description: 28S ribosomal protein S5, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5REJ1]

Sequence

>retro_pabe_2574
ACTGCAGATGAGCTGTGGAAAGGTGTTTTAGCAGAGACTGGTGCTGGAGCAAGAAAAGGAAGAGGCAGCAGAACTAAAAA
GAAGAGAAGAAAGGATTTGAACAGGGGTCAGATCATTGGTGAAGGGCATTATGGTTTCTGCGGCCTGGTCTGAATGTCCC
TCTTATTAAAAATGGAGCAGTACAGATCATTGCCCAAAAAAGCAAGGAAGAACAGAACGAGGAGGCCAACATGACCCAGC
AGAGAGAAGAATGGGACTGGAAGAGGAGGATGAAGATAAATGAGAGTGAGGATGCAGTGGAAACTTGTGGGGAGGCATCA
GTCTTAGCCATCTGACCCTGGTCCCAACAGAGAAACATATGGCAATTTTGATACCAGGATACTCGAGGTAGGAAATGTTT
TCAATAGGACAGCAAAAGAGGGAAGAAAGAGATTGGTAGGTGTCCTGCAGGCTGTGGGGAAGGGACAACGAGCTTCAAGT
TTTGCTGTTGCGAAAGCCACTAAATGGATAGATGCTTTCAGAAAAGCAAAGAATAGAGCAATTCACTATTTGCATTATGT
AGAACGATATGAAGACCATACAATATTCCATGATACTTCATTAAGATTTAAAAGGAGGCATATCAGGATGAAGAAACAAC
CCACAGGTTACGAGGTCTGCTGCCACAGGGCCATCAACACCATATGCCAGCTCGCTGGCATCAAAGACATGTATGCCAAG
GTCTCTGGGTCCATCGGTACGCTCCCCCTCACCTGGGGCCTCTTCCACGGGCTCTCA

Alignment

ORF - retro_pabe_2574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.97 %
• Parental protein coverage: 60.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TADELWKGALAETGAGAKKGRGKRTKKKKRKDLNRGQIIGEGRYGF-LWPGLNVPVMKNGTVQTIAQRSK
          TADELWKG.LAETGAGA.KGRG.RTKKK.RKDLNRGQIIGEG.YGF.L.PGLNVP..KNG.VQ.IAQ.SK
Retrocopy TADELWKGVLAETGAGARKGRGSRTKKKRRKDLNRGQIIGEGHYGF<LRPGLNVPLIKNGAVQIIAQKSK

Parental  EEQEKVEADVIQQREEWERKKKMKV-KRERGWSGNSWGGLSLG-PPDPGPSGETYEDFDTRILEVRNVFT
          EEQ...EA...QQREEW..K..MK..K.E.G.SGN.WGG.SL..P.DPGP..ETY..FDTRILEV.NVF.
Retrocopy EEQNE-EANMTQQREEWDWKRRMKI<K*E*GCSGNLWGGISLS<PSDPGPNRETYGNFDTRILEVGNVFN

Parental  MTAKEGRRKSIRVLVAVGNGKGAAGFAIGKATDRMDAFRKAKNRAVHHLYYIERYEDHTIFHDISLRFKR
          .TAKEGR.....VL.AVG.G..A..FA..KAT...DAFRKAKNRA.H.L.Y.ERYEDHTIFHD.SLRFKR
Retrocopy RTAKEGRKRLVGVLQAVGKGQRASSFAVAKATKWIDAFRKAKNRAIHYLHYVERYEDHTIFHDTSLRFKR

Parental  THIKMKKQPKGYGLRCHRAIITICRLIGIKDMYAKVSGSTNMLSLTQGLFHGLS
          .HI.MKKQP.GY...CHRAI.TIC.L.GIKDMYAKVSGS...L.LT.GLFHGLS
Retrocopy RHIRMKKQPTGYEVCCHRAINTICQLAGIKDMYAKVSGSIGTLPLTWGLFHGLS

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	24.77 RPM
SRP007412_cerebellum	0.00 RPM	32.83 RPM
SRP007412_heart	0.00 RPM	36.85 RPM
SRP007412_kidney	0.00 RPM	41.14 RPM
SRP007412_liver	0.00 RPM	43.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2574 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2574 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3116
Pan troglodytes	retro_ptro_2107
Gorilla gorilla	retro_ggor_2139
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,