RetrogeneDB ID: retro_ptro_1840

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:163882188..163884110(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000005970
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ptro_1840
TCGGACAAACACTTCCACGAGGACTATGTAGAGAAGCCCTTGAAGCTGGTCCTCAAAGTAGGAGGGAACGAAGTCACCGA
ACTCTCCACGGGCAGCTCGGGGCACGACTCCAGCCTCTTCGAAGACAAAAACGATCATGACAAACACAAGGACAGAAAGC
GGAAAAAGAGAAAGAAAGGAGAGAAGCAGATTCCAGGGGAAGAAAAGGGGAGAAAACGGAGAAGAGTTAAGGAGGATAAA
AAGAAGCGAGATCGAGACCGGGTGGAGAATGAGGCAGAAAAAGACCTCCAGTGTCACGCCCCTGTGAGATTAGACTTGCC
CCCTGAGAAGCCTCTCACAAGCTCTTTAGCCAAACAAGAAGTAGAACAGACACCCCTTCAAGAAGCTTTGAATCAACTGA
TGAGACAATTGTAGAGAAAAGATCCAAGTGCTTTCTTTTCATTTCCTGCGGCTGATTTTATTGCTCCTGGCTACTCCATG
ATCATTAAACACCCAATGGATTTTAGTACCATGAAAGAAAAGATCAAGAACAATGACTATCAGTCCATAGAAGAACTAAA
GGATAACTTCAAACTAATGTGTACTAATGCCATGATTTACAATAAACCAGAGACCATTTATTATAAAGCTGCAAAGAAGC
TGTTGCACTCAGGGATGAAAATTCTTAACCAGGAAAGAATTCAGAGCCTGAAGCAGAGCATAGACTTCATGGCTGACTTG
CAGAAAACTCGAAAGCAGAAAGATGGAACAGACACCTCACAGAGTGGGGAGGACGGAGGCTGCTGGCAGAGAGAGAGAGA
GGACTCTGGAGATGCCGAAGCACATGCCTTCAAGAGTCCCAGCAAAGAAAATAAAAAGAAAGACAAAGATATGCTTGAAG
ATAAGTTTAAAAGCAATAATTTAGAGAGAAAGCAGGAGCAGCTTGACCGCATTGTGAAGGAATCTGGAGGAAAACTGACC
AGGCGGCTTGTGAACAGTCAGTGCGAATTTGAAAGAAGAAAACCAGGTGGAACAACGACATTGGGACTTCTCCATCCTGA
GGATCCCATTGTAGGAGAGCCAGGCTACTGCCCTGTGAGACTGGGAATGACAACTGGAAGACTTCAGTCTGGAGTGAATA
CTTTGCAGGGGTTCAAAGAGGATAAAAGGAACAAAGTCACTCCAGTGTTATATTTGAATTATGGGCCCTACGGTTCTTAT
GCAACGCATTATGACTCCACATTTGCGAATATCAGCAAGGATGATTCTGATTTAATCTATTCAACCTATGCGGAAGACTC
TGATCTTCCAAGCGATTTCAGCAGCCATGAGTTTTTGGCCACGTGCCAAGATTATCCGTATGTCATGGCAGATAGTTTAC
TGGATGTTTTAACAAAAGGAGGGCATTCCAGGACCCTACAAGAGATGGAGATGTCATTGCCTGAAGATGAAGGCCATACT
AAGACACTTGACACAGCAAAAGAAATGGAGATTACAGAAGTAGAGCCGCCAGGGCGTTGGAGTCCAATACTCAAGACAGG
TTCATAGCGCTGAAAGCAGTAACAAATTTTGGCGTTCCAGTTGAAGTTTTTGACTCTGAAGAAGCTGAAATATTCCAGAA
GAAACTTGATGAGACCACCAGATCGCTCAGGGAACTCCAGGAAGCCCAGAATGAACGTTTGAGCACCAGACCCCCTCCCA
ACATGATCTGTCTCTTGGGTCCCTCATACAGAGAAATGCATCTTGCTGAACAAGTGACCAATAATCTTAAAGAACTTGCA
CAGCAAGTAACTCCAGGTGATATCGTAAGCACGTATGGAGTTCGAAAAGCAATGGGGATTTCCATTCCTTCCCCCGTCAT
GGAAAACAACTTTGTGGATTTGACAGAAGACACTGAAGAACCTAAAAAGGCGGATGTTGCTGAGTGTGGACCTGGTGGAA
GT

Alignment

ORF - retro_ptro_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 98.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDKHLYEEYVEKPLKLVLKVGGNEVTELSTGSSGHDSSLFEDKNDHDKHKDRKRKKRKKGEKQIPGEEKG
          SDKH..E.YVEKPLKLVLKVGGNEVTELSTGSSGHDSSLFEDKNDHDKHKDRKRK...............
Retrocopy SDKHFHEDYVEKPLKLVLKVGGNEVTELSTGSSGHDSSLFEDKNDHDKHKDRKRKXXXXXXXXXXXXXXX

Parental  RKRRRVKEDKKKRDRDRVENEAEKDLQCHAPVRLDLPPEKPLTSSLAKQEEVEQTPLQEALNQLMRQLQR
          .....VKEDKKKRDRDRVENEAEKDLQCHAPVRLDLPPEKPLTSSLAKQE.VEQTPLQEALNQLMRQL.R
Retrocopy XXXXXVKEDKKKRDRDRVENEAEKDLQCHAPVRLDLPPEKPLTSSLAKQE-VEQTPLQEALNQLMRQL*R

Parental  KDPSAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYK
          KDPSAFFSFP..DFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYK
Retrocopy KDPSAFFSFPAADFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYK

Parental  AAKKLLHSGMKILSQERIQSLKQSIDFMADLQKTRKQKDGTDTSQSGEDGGCWQREREDSGDVEAHAFKS
          AAKKLLHSGMKIL.QERIQSLKQSIDFMADLQKTRKQKDGTDTSQSGEDGGCW.....DSGD.EAHAFKS
Retrocopy AAKKLLHSGMKILNQERIQSLKQSIDFMADLQKTRKQKDGTDTSQSGEDGGCWXXXXXDSGDAEAHAFKS

Parental  PSKENKKKDKDMLEDKFKSNNLEREQEQLDRIVKESGGKLTRRLVNSQCEFERRKPDGTTTLGLLHPVDP
          PSKENKKKDKDMLEDKFKSNNLER.QEQLDRIVKESGGKLTRRLVNSQCEFERRKP.GTTTLGLLHP.DP
Retrocopy PSKENKKKDKDMLEDKFKSNNLERKQEQLDRIVKESGGKLTRRLVNSQCEFERRKPGGTTTLGLLHPEDP

Parental  IVGEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPYSSYAPHYDSTFANISKDDSDLI
          IVGEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPY.SYA.HYDSTFANISKDDSDLI
Retrocopy IVGEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPYGSYATHYDSTFANISKDDSDLI

Parental  YSTYGEDSDLPSDFSIHEFLATCQDYPYVMADSLLDVLTKGGHSRTLQEMEMSLPEGEGHTRTLDTAKEM
          YSTY.EDSDLPSDFS.HEFLATCQDYPYVMADSLLDVLTKGGHSRTLQEMEMSLPE.EGHT.TLDTAKEM
Retrocopy YSTYAEDSDLPSDFSSHEFLATCQDYPYVMADSLLDVLTKGGHSRTLQEMEMSLPEDEGHTKTLDTAKEM

Parental  EQITEVEPPGR-LDSSTQDRLIALKAVTNFGVPVEVFDSEEAEIFQKKLDETTRLLRELQEAQNERLSTR
          E.ITEVEPPGR.L.S.TQDR.IALKAVTNFGVPVEVFDSEEAEIFQKKLDETTR.LRELQEAQNERLSTR
Retrocopy E-ITEVEPPGR<LESNTQDRFIALKAVTNFGVPVEVFDSEEAEIFQKKLDETTRSLRELQEAQNERLSTR

Parental  PPPNMICLLGPSYREMHLAEQVTSNLKELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEE
          PPPNMICLLGPSYREMHLAEQVT.NLKELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEE
Retrocopy PPPNMICLLGPSYREMHLAEQVTNNLKELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEE

Parental  PKKTDVAECGPGGS
          PKK.DVAECGPGGS
Retrocopy PKKADVAECGPGGS

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	1.07 RPM	21.81 RPM
SRP007412_cerebellum	0.25 RPM	31.91 RPM
SRP007412_heart	0.06 RPM	26.49 RPM
SRP007412_kidney	0.03 RPM	33.21 RPM
SRP007412_liver	0.10 RPM	17.48 RPM
SRP007412_testis	3.48 RPM	74.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1840 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1840 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2723
Gorilla gorilla	retro_ggor_1895

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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,