RetrogeneDB ID: retro_ptro_2089

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:128217145..128217805(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM248
• Ensembl ID: ENSPTRG00000019253
• Aliases: None
• Description: transmembrane protein 248 [Source:HGNC Symbol;Acc:25476]

Sequence

>retro_ptro_2089
GCCAGAACATCCACCAGGTCTTCCCAGGCCCTGGAGGATTCAGGCCCAGTTAACATCTCAGTCAAAATCACCCTAACCCT
GGACCCACTCAAATTATTTGGAGGGTACTCTCATGGCATCACTCATCTGTATTCAGTCATTTTAGGTCATCAGATTGGAC
TTTCCGACAGAGAAGCCCACGAAGAGGTAAATATTACCTTTACTCTGCCTGCAGCTTGGACATCAGATAGCTGTGCTCTT
GATGGTCACCATGAGCAGATGGTGTTCACAGCCTGCATGATCCTCACGGACAGCCCGGGTGTGTTCCCCATCACTGTGCA
GCCACCGCACCGTGTTTCTGACACATACAGCAATGCCACACTCTGGTGCAAGATCTTTAGAACTGACAGAAAGGCCAACA
CAGAATACGCTCAAGATTACAGCCTTTTCTGTTGTTAGAAAAGGCCCATTGAAAAAGACTATCATGTTTTTAATCCCAAG
CATACAGTTATTGCTCCAGATGATGACTGTTCATTAATAAATTTGCATCTAATGCATACCAGTTACTTCCTCCTCATGAT
GGTGATAATAGTGTTTTGCTATACTGTTATCAAAGGCAGACCCAACAAATTGTGTCAGAGCAATCCTAAATATTGTCCTG
AGAAGACAGCTTTGGCTGAC

Alignment

ORF - retro_ptro_2089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.82 %
• Parental protein coverage: 70.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARASTQSPQALEDSGPVNISVSITLTLDPLKPFGGYSRNVTHLYSTILGHQIGLSGREAHEEINITFTLP
          AR.ST.S.QALEDSGPVNISV.ITLTLDPLK.FGGYS...THLYS.ILGHQIGLS.REAHEE.NITFTLP
Retrocopy ARTSTRSSQALEDSGPVNISVKITLTLDPLKLFGGYSHGITHLYSVILGHQIGLSDREAHEEVNITFTLP

Parental  TAWSSDDCALHGHCEQVVFTACMTLTASPGVFPVTVQPPHCVPDTYSNATLWYKIFTTARDANTKYAQDY
          .AW.SD.CAL.GH.EQ.VFTACM.LT.SPGVFP.TVQPPH.V.DTYSNATLW.KIF.T.R.ANT.YAQDY
Retrocopy AAWTSDSCALDGHHEQMVFTACMILTDSPGVFPITVQPPHRVSDTYSNATLWCKIFRTDRKANTEYAQDY

Parental  NPFWCYKGAIGKVYHALNPKLTVIVPDDDRSLINLHLMHTSYFLFVMVITMFCYAVIKGRPSKLRQSNPE
          ..F.C.K..I.K.YH..NPK.TVI.PDDD.SLINLHLMHTSYFL..MVI..FCY.VIKGRP.KL.QSNP.
Retrocopy SLFCC*KRPIEKDYHVFNPKHTVIAPDDDCSLINLHLMHTSYFLLMMVIIVFCYTVIKGRPNKLCQSNPK

Parental  FCPEKVALAE
          .CPEK.ALA.
Retrocopy YCPEKTALAD

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	20.54 RPM
SRP007412_cerebellum	0.00 RPM	29.00 RPM
SRP007412_heart	0.00 RPM	13.84 RPM
SRP007412_kidney	0.00 RPM	34.91 RPM
SRP007412_liver	0.00 RPM	29.23 RPM
SRP007412_testis	0.00 RPM	31.51 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2089 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2089 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3093
Gorilla gorilla	retro_ggor_2124
Macaca mulatta	retro_mmul_1973

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004278	1 retrocopy	retro_cjac_2145,
Cavia porcellus	ENSCPOG00000000830	1 retrocopy	retro_cpor_330,
Echinops telfairi	ENSETEG00000015971	1 retrocopy	retro_etel_2097,
Homo sapiens	ENSG00000106609	1 retrocopy	retro_hsap_3093,
Gorilla gorilla	ENSGGOG00000022776	1 retrocopy	retro_ggor_2124,
Myotis lucifugus	ENSMLUG00000000616	1 retrocopy	retro_mluc_1974,
Macaca mulatta	ENSMMUG00000015843	1 retrocopy	retro_mmul_1973,
Nomascus leucogenys	ENSNLEG00000013326	1 retrocopy	retro_nleu_2235,
Pan troglodytes	ENSPTRG00000019253	1 retrocopy	retro_ptro_2089 ,
Pteropus vampyrus	ENSPVAG00000002978	2 retrocopies	retro_pvam_988, retro_pvam_997,
Sorex araneus	ENSSARG00000001884	1 retrocopy	retro_sara_563,