RetrogeneDB ID: retro_ptro_178

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:104581784..104582542(+)
• Located in intron of: ENSPTRG00000023940

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSPTRG00000018890
• Aliases: ACTB, beta-actin
• Description: Pan troglodytes actin, beta (ACTB), mRNA. [Source:RefSeq mRNA;Acc:NM_001009945]

Sequence

>retro_ptro_178
ATGGAAGAAGAGATTGCCGCACTGGTGATTGACAATGGCTCCAGCATGTGCAAAGCTGGCTTTGCTGGGGACGACAACCC
CCAGCCATGTTTCCTTCCATCATCGGTGCCCCCGGCACCAGGGCATGATGGGTGGGCATGGGCCAGAGGGACTCCTATGG
GGGCTACATGGCTGAGAGCAAGCACAGCATCCTGACCCTGAAGTACCCCCATTAAGCATGGTATCATGACCAACTGGGAT
GACATAGAGAAGATCTGGCATCACACCTTCTACAAGGGACTGCACATGGCCTTGGAGGAGCACCTGGTGCTGCTGACCGA
GGACCCCCTGAACCTCAAGGCCAACAGAGAGAAGATGACTCAGATCATGTTTGATACCTTCAACACCCTGGCCATGTACG
TGGCCATCCAGGCTATGCTGTCCCTCTACACCTGTGGTTGCACACTGGCATTGTCATGGGCTCTGGAGATGGGGTCACCC
ACATGGTGCCCATCTATAAGGGCTACGCCCTCCCTGACACCATTCTGCATCTGGACCTGGCTGGCCAGGACCTGACCAAC
TACCTCATGAAGATCCTTACCAAGGTTGGCTATAGCTTCAGCACCACTGCCGAGCGGGAGATCAGACACTACGTCAAGGA
GAAACTGTGCTATGTTGCCCTGGACTTTGAGCAGTAGATGGCCACTGCCACATCCTCCTCCTCCCTGGAGAAGAGATATG
AGCTGCCTGATGGCCATGTCATCACCATCGGCAATGAG

Alignment

ORF - retro_ptro_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.13 %
• Parental protein coverage: 67.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MDDDIAALVVDNGSGMCKAGFAGDDAPR-AVFPSIVGRP-RHQGVM-VGMGQKDSYVGDEAQSKRGILTL
          M...IAALV.DNGS.MCKAGFAGDD.P..A.FPSI.G.P.RHQG.M.VGMGQ.DSY.G..A.SK..ILTL
Retrocopy MEEEIAALVIDNGSSMCKAGFAGDDNPQ<AMFPSIIGAP<RHQGMM>VGMGQRDSYGGYMAESKHSILTL

Parental  KYP-IEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAI
          KYP.I.HGI.TNWDD.EKIWHHTFY..L..A.EEH.VLLTE.PLN.KANREKMTQIMF.TFNT.AMYVAI
Retrocopy KYP>IKHGIMTNWDDIEKIWHHTFYKGLHMALEEHLVLLTEDPLNLKANREKMTQIMFDTFNTLAMYVAI

Parental  QAVLSLYASGRT-TGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAE
          QA.LSLY..G.T.TGIVM.SGDGVTH.VPIY.GYALP..IL.LDLAG.DLT.YLMKILT..GYSF.TTAE
Retrocopy QAMLSLYTCGCT<TGIVMGSGDGVTHMVPIYKGYALPDTILHLDLAGQDLTNYLMKILTKVGYSFSTTAE

Parental  REIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNE
          REI....KEKLCYVALDFEQ.MATA.SSSSLEK.YELPDG.VITIGNE
Retrocopy REIRHYVKEKLCYVALDFEQ*MATATSSSSLEKRYELPDGHVITIGNE

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	4.75 RPM	1976.36 RPM
SRP007412_cerebellum	5.31 RPM	1129.84 RPM
SRP007412_heart	0.87 RPM	382.11 RPM
SRP007412_kidney	4.86 RPM	1474.96 RPM
SRP007412_liver	1.83 RPM	1774.09 RPM
SRP007412_testis	0.42 RPM	315.31 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_178 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_178 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pan troglodytes	ENSPTRG00000002894	1 retrocopy	retro_ptro_1567,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178 , retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,