RetrogeneDB ID: retro_ptro_757

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:40857968..40858344(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BOD1
• Ensembl ID: ENSPTRG00000017544
• Aliases: None
• Description: biorientation of chromosomes in cell division 1 [Source:HGNC Symbol;Acc:25114]

Sequence

>retro_ptro_757
ACCCGCCGCTCATCCTGGAGCGGCTCAGGGCCGTTTAGCAGCTTCCGCAGGTGCTGCCTGGCCCCCGTAGACACCAAGCC
AGCTTATCAAAATTAAGGCAGAAGGCCCAGCATTCGGTGTCCACACACCTGGACAAGCAGGAATGGAATCCTACAATGCG
CAAAAACTGATTGCGAAGTGGCCTGAGGCAGAGTGTTTTTCAGTCAGGGACGTTGAAAGCTGGAGTTGACGGGGTTCTTT
ATCAGATGGTGGATCCAGAACTAAACCACATCCCCAGGCCACCAGTGGAATGAGCAATTCACGAGATCCTGGGCGCCCAG
AAGACAGCAATGGTGCCAGTGCCCCCTCAGAGCCCAAAGACCAGTACCCTCCAGCC

Alignment

ORF - retro_ptro_757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.41 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SQASAGASRGLFDSFRRDCLADVDTKPAYQN-LRQKVDNFVSTHLDKQEWNPTMNKNQLRNGLRQSVVQS
          ...S.....G.F.SFRR.CLA.VDTKPAYQN.LRQK....VSTHLDKQEWNPTM.KN.LR.GLRQSV.QS
Retrocopy TRRSSWSGSGPFSSFRRCCLAPVDTKPAYQN<LRQKAQHSVSTHLDKQEWNPTMRKN*LRSGLRQSVFQS

Parental  GMLEAGVDRIISQVVDPKLNHIFRPQIERAIHEFLAAQKKAAVPAP-PPEPEGQDPPA
          G.L.AGVD....Q.VDP.LNHI.RP..E.AIHE.L.AQK.A.VP.P.P.EP..Q.PPA
Retrocopy GTLKAGVDGVLYQMVDPELNHIPRPPVE*AIHEILGAQKTAMVPVP<PSEPKDQYPPA

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	0.07 RPM	8.01 RPM
SRP007412_cerebellum	0.22 RPM	10.22 RPM
SRP007412_heart	0.00 RPM	10.14 RPM
SRP007412_kidney	0.08 RPM	8.76 RPM
SRP007412_liver	0.00 RPM	8.48 RPM
SRP007412_testis	0.11 RPM	24.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_757 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_757 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_757 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_993
Gorilla gorilla	retro_ggor_794
Macaca mulatta	retro_mmul_803

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000034598	1 retrocopy	retro_btau_663,
Canis familiaris	ENSCAFG00000016776	1 retrocopy	retro_cfam_1374,
Callithrix jacchus	ENSCJAG00000031971	4 retrocopies	retro_cjac_1154, retro_cjac_1515, retro_cjac_1536, retro_cjac_953,
Homo sapiens	ENSG00000145919	3 retrocopies	retro_hsap_102, retro_hsap_1867, retro_hsap_993,
Gorilla gorilla	ENSGGOG00000010925	2 retrocopies	retro_ggor_1365, retro_ggor_794,
Microcebus murinus	ENSMICG00000002626	1 retrocopy	retro_mmur_1126,
Macaca mulatta	ENSMMUG00000013793	2 retrocopies	retro_mmul_803, retro_mmul_869,
Mus musculus	ENSMUSG00000044502	1 retrocopy	retro_mmus_3661,
Nomascus leucogenys	ENSNLEG00000000476	1 retrocopy	retro_nleu_1224,
Oryctolagus cuniculus	ENSOCUG00000014283	1 retrocopy	retro_ocun_1071,
Otolemur garnettii	ENSOGAG00000001107	3 retrocopies	retro_ogar_1477, retro_ogar_2663, retro_ogar_3112,
Pongo abelii	ENSPPYG00000016057	2 retrocopies	retro_pabe_1567, retro_pabe_1587,
Pan troglodytes	ENSPTRG00000017544	2 retrocopies	retro_ptro_1282, retro_ptro_757 ,
Ictidomys tridecemlineatus	ENSSTOG00000013505	1 retrocopy	retro_itri_1164,
Tupaia belangeri	ENSTBEG00000014046	1 retrocopy	retro_tbel_3451,
Tarsius syrichta	ENSTSYG00000007617	1 retrocopy	retro_tsyr_818,
Tursiops truncatus	ENSTTRG00000000384	2 retrocopies	retro_ttru_1004, retro_ttru_457,
Vicugna pacos	ENSVPAG00000004260	1 retrocopy	retro_vpac_452,