RetrogeneDB ID: retro_ptro_2384

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:119647004..119648146(+)
• Located in intron of: ENSPTRG00000018549

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRD7
• Ensembl ID: ENSPTRG00000008103
• Aliases: None
• Description: Bromodomain containing 7 [Source:UniProtKB/TrEMBL;Acc:K7B3V4]

Sequence

>retro_ptro_2384
GAAGAACTAATGGATAACTTCAAACCAATATGTACTAATGCCATGATTTACAACAAACCAGAGACCACTTATTATAAAGC
TGCAAAGAAGCTGTTACACTCAGAGATGAAAATTTTTAGCCAGGAAAAAATTCAGAGCCTGAAGCAGAGCACAGACTTCA
TGGCTAACTTGAAAAAACTTGAAAGCAGAAAGACAGAACAGACATCTCACAGAGTGGGGAGGATGGAGGCTACTGGCTGA
GAGAGAGAGAGAGAGAGAGAGGACTCTGGAGATGCCGAAGCACAAGCCTTCAAGAGTCCCAGCAAAGAAAATAAAAAGAA
AGACAAAGATATGCTTTTAAGTTTAAAAGCAGTAATTTAGAGAGACAGTAGGAGCAGCTTGACTGCATCATGAAGGAATC
TGGAGGAAAACTGACCAGGTGGCTTGTTAACAGTCAGCGGGAATTTGAAAGAAGAAAACCAGATGGAACAAGAAGACTGG
GACTTCCCCATCCCGTGGATCCCATTGTAGGAGAGCCAGAATACTGCCCTATGAGACTGGGAATGACAACTGGAAGACTT
CAGTCTGGAGTGAATACTCTGCAGGGGTTCAAAGAGGATAAAAGGAACAAAGTAACTCCAGGGTTATATTTGAATTATGG
ACCCTGGAGTTCTTATGTACTGCATTATGACTCCACATTTACGAATATCAGCAAGGATAATTCAGATTTAATCTATGCAA
TCTATGGGGGAAGACTGATCTTCCAAGCAATTTCAGCAACCATGAGTTTCTGGCCCCATGCCAAGATTACCCATATGTTA
TGACAGATAGTTTGCTGGATGTTTTAACAAAAGGAGGGGATTCCAGGGCCCTATAAGAGTTGGAGATATCACCTGAAGAT
GAAGGCCATACTAGGACACTTGACACAGCAAAACAAATGGAGATTACACAAGTAGAGCCAGCAGGACATTTGGACTCTAA
TACTCAAGATAGGCTCGTGGCACTGAAAGCAGTAACAAACTTTGGCACTCCGGTTGAAGTTTTTGACTCTTGAAGAAGCT
GAAGTATTCCAGAAGAAACCTGATGAGACCAACAAATTGCTCAGGGAGCTCCAGCTCAATGAGCATTTGAACACCTGACC
CCTTCCCAATATGATGTCTCTT

Alignment

ORF - retro_ptro_2384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.2 %
• Parental protein coverage: 58.74 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQSIDFMAD-LQKTRKQKDGTDT
          EEL.DNFK..CTNAMIYNKPET.YYKAAKKLLHS.MKI.SQE.IQSLKQS.DFMA..L.KT.KQKD.TD.
Retrocopy EELMDNFKPICTNAMIYNKPETTYYKAAKKLLHSEMKIFSQEKIQSLKQSTDFMAN<LEKT*KQKDRTDI

Parental  SQSGEDGGCWQREREDSGDVEAHAFKSPSKENKKKDKDMLEDKFK--SNNLEREQEQLDRIVKESGGKLT
          SQSGEDGG.W................S.......K.K......FK..S.NLER..EQLD.I.KESGGKLT
Retrocopy SQSGEDGGYWXXXXXXXXXLWRCRSTSLQESQQRK*KERQRYAFKFKSSNLERQ*EQLDCIMKESGGKLT

Parental  RRLVNSQCEFERRKPDGTTTLGLLHPVDPIVGEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVL
          R.LVNSQ.EFERRKPDGT..LGL.HPVDPIVGEP.YCP.RLGMTTGRLQSGVNTLQGFKEDKRNKVTP.L
Retrocopy RWLVNSQREFERRKPDGTRRLGLPHPVDPIVGEPEYCPMRLGMTTGRLQSGVNTLQGFKEDKRNKVTPGL

Parental  YLNYGPYSSYAPHYDSTFANISKDDSDLIYSTYG-EDSDLPSDFSIHEFLATCQDYPYVMADSLLDVLTK
          YLNYGP.SSY..HYDSTF.NISKD.SDLIY..YG....DLPS.FS.HEFLA.CQDYPYVM.DSLLDVLTK
Retrocopy YLNYGPWSSYVLHYDSTFTNISKDNSDLIYAIYG<GKTDLPSNFSNHEFLAPCQDYPYVMTDSLLDVLTK

Parental  GGHSRTLQEMEMSLPEGEGHTRTLDTAKEMEQITEVEPPGRLDSSTQDRLIALKAVTNFGVPVEVFDS-E
          GG.SR.L.E.E.S.PE.EGHTRTLDTAK.ME.IT.VEP.G.LDS.TQDRL.ALKAVTNFG.PVEVFDS.E
Retrocopy GGDSRAL*ELEIS-PEDEGHTRTLDTAKQME-ITQVEPAGHLDSNTQDRLVALKAVTNFGTPVEVFDS>E

Parental  EAEIFQKKLDETTRLLRELQEAQNERLSTRPPPNMICL
          EAE.FQKK.DET..LLRELQ...NE.L.T.P.PNM..L
Retrocopy EAEVFQKKPDETNKLLRELQ--LNEHLNT*PLPNMMSL

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	0.13 RPM	21.81 RPM
SRP007412_cerebellum	0.25 RPM	31.91 RPM
SRP007412_heart	0.00 RPM	26.49 RPM
SRP007412_kidney	0.00 RPM	33.21 RPM
SRP007412_liver	0.00 RPM	17.48 RPM
SRP007412_testis	0.74 RPM	74.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2384 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2384 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_2372

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009355	1 retrocopy	retro_chof_2431,
Callithrix jacchus	ENSCJAG00000001832	1 retrocopy	retro_cjac_2372,
Homo sapiens	ENSG00000166164	2 retrocopies	retro_hsap_2723, retro_hsap_3507,
Gorilla gorilla	ENSGGOG00000014824	2 retrocopies	retro_ggor_1895, retro_ggor_2372,
Monodelphis domestica	ENSMODG00000013057	1 retrocopy	retro_mdom_152,
Otolemur garnettii	ENSOGAG00000011289	2 retrocopies	retro_ogar_326, retro_ogar_438,
Pan troglodytes	ENSPTRG00000008103	3 retrocopies	retro_ptro_1840, retro_ptro_2379, retro_ptro_2384 ,
Pan troglodytes	ENSPTRG00000016688	1 retrocopy	retro_ptro_2061,