RetrogeneDB ID: retro_ptro_2990

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390401.1:91830..92369(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM98
• Ensembl ID: ENSPTRG00000008993
• Aliases: None
• Description: None

Sequence

>retro_ptro_2990
AAGGCCACAGTGATTGTTGCCATAAGCGTGCTGGCTACCATCTTTCTGGCTTTGTTTGCAGTCTTGGTGGTGGTTTGAGT
GCAGCGCTACCACTGGCCAGGAGACCTGCCGCAGCGCTATGATTCCAAGCCCACTATGAGTCTCTTGGGTGCCATGGAGA
CCCAATCTGAGCTCTCTGAGTTAGAACTAGATGATGTCATCATCGCCCACTCTGGCATAGAGCCCATTCTGGAGAATGAA
GACTGGATCTAGGATGCCTTGGGTCTCATGTCCCACTGCATTGTCATCTTGAAGATTTGTCACACTTTGAGAGAAAAACT
TGTTGCCATGACAACGGGCTCAGAGGCTGAGAAGAAGACTTCAGCCACTGTCAGCAGCATCATTGTGGTGGCCAAGTGGA
TCATCCCCAGAGTAGATGATGTTGTGAAATCAGTGTACCATCTGTTAAGCACCAAGCTCCTGGATGTGAGTACGACTGCC
CTGCTCCTGTCAGTCATCAGGTGCTGGTAACCAGAAATGCCTGCCATCTGAACAGGGGC

Alignment

ORF - retro_ptro_2990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.98 %
• Parental protein coverage: 80.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETVVIVAIGVLATIFLASFAALVLVCRQRYCRPRDLLQRYDSKPIVDLIGAMETQSEPSELELDDVVITN
          ...VIVAI.VLATIFLA.FA.LV.V..QRY..P.DL.QRYDSKP...L.GAMETQSE.SELELDDV.I..
Retrocopy KATVIVAISVLATIFLALFAVLVVV*VQRYHWPGDLPQRYDSKPTMSLLGAMETQSELSELELDDVIIAH

Parental  PHIEAILENEDWIEDASGLMSHCIAILKICHTLTEKLVAMTMGSGAKMKTSASVSDIIVVAKRISPRVDD
          ..IE.ILENEDWI.DA.GLMSHCI.ILKICHTL.EKLVAMT.GS.A..KTSA.VS.IIVVAK.I.PRVDD
Retrocopy SGIEPILENEDWI*DALGLMSHCIVILKICHTLREKLVAMTTGSEAEKKTSATVSSIIVVAKWIIPRVDD

Parental  VVKSMYPPLDPKLLDARTTALLL-SVSHLVLVTRNACHLTGG
          VVKS.Y..L..KLLD...T..LL..VSH.VLVTRNACHL..G
Retrocopy VVKSVYHLLSTKLLDV-STTALL<PVSHQVLVTRNACHLNRG

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	24.15 RPM
SRP007412_cerebellum	0.00 RPM	20.43 RPM
SRP007412_heart	0.00 RPM	5.04 RPM
SRP007412_kidney	0.00 RPM	42.44 RPM
SRP007412_liver	0.00 RPM	15.91 RPM
SRP007412_testis	0.32 RPM	3.79 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2990 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2990 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3605
Pan troglodytes	retro_ptro_2436
Gorilla gorilla	retro_ggor_2432
Pongo abelii	retro_pabe_2961
Macaca mulatta	retro_mmul_1835
Callithrix jacchus	retro_cjac_2447

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014550	1 retrocopy	retro_cjac_2447,
Homo sapiens	ENSG00000006042	2 retrocopies	retro_hsap_1421, retro_hsap_3605,
Gorilla gorilla	ENSGGOG00000013333	2 retrocopies	retro_ggor_1098, retro_ggor_2432,
Myotis lucifugus	ENSMLUG00000001191	1 retrocopy	retro_mluc_130,
Macaca mulatta	ENSMMUG00000022356	2 retrocopies	retro_mmul_1835, retro_mmul_2256,
Nomascus leucogenys	ENSNLEG00000006038	3 retrocopies	retro_nleu_1233, retro_nleu_1840, retro_nleu_2635,
Pongo abelii	ENSPPYG00000008166	2 retrocopies	retro_pabe_1175, retro_pabe_2961,
Pan troglodytes	ENSPTRG00000008993	3 retrocopies	retro_ptro_2436, retro_ptro_2990 , retro_ptro_971,