RetrogeneDB ID: retro_ptro_2379

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:112530285..112531702(+)
• Located in intron of: ENSPTRG00000018508

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_2379
ATGAAAGAAAAGATCAAGAACAATGACTACCAGTCCATAGAAAAACTAAAGGATATTTTCAAACTAATGTGTACTAATGC
CATGATTTACAATAAACCAGAGACCATTTATTATAAAGCTGCAAAGAAGCGGTTGCACTCGGGGATGAAAATTCTTAGAC
ATGAAAGAATTCAGAGCCTGAAGCAGAGCATAGACTTCATGGCTGACTTGCAGAAAACTCAAAAGCAGGAAGACAGAACA
GACACCTCGCAGAGTGGGGAGGACAGAGGCTGCTGGCCGAGAAGAGAGAGGACTCTGGAGATGCCAAAGCACACGCCTTC
AAGAGTCCCAGCAAAGAAAATAAAAAGAAAGACAAAGACATGCTTGAAGGTAAGTTTAAAAGCAATAATTTAGAGAGAGC
GCAGGGGCAGCTTGACGGCATCGTGAAGGAATCTGGAGGAAAGCTGACCAGGCGGCTTGTGAACAGTCAGTGCAAATTGG
AAAGAAGAAAACCAGACGGAACAACAATGTTGGGACTTCTCCATCCTGTGGATCTCATTGTAGGAGAGCCAGGCTACTGC
CCTGTGAGACTGGGAATGACAACTGGAAGACTTCAGTCTGGTGTGAATACTTTGCAGGGGTTCAAAGAGGACAAAAGAAC
AAAGTCACTCCAGTGTTATATTTGAATTATGGGCCCTACAGTTCTTATGCACCGCATTATGACTCCATATATGCAAATAT
CAACAAGAATGATTCTGATTTAATCTATTCAACCTATGGGGAAGACACAGATCTTCCAAGCGATCTCAGCAGCCATGAGT
TTTTGGCCACGTGCCAAGATTATCCATCTGTGATGGCAGATAGTTTACTGGATGTTTTAACAAAAGGAGGGCATTCCAGG
ACCCTACAAGAGATTTAGATGTCACTGCCTGAAGATGGAAGGCCATACTAGGACACCTGACACAGCAAAAGAAATGGAGA
TTACAGAAGTAGAGCCACCAGGATATCTGGACTCCAATACTTCAAGACAGGCTCATAGCGCTGAAAGCAGTAACAAACTT
TGGCGTTCCGGTTAAAGTTTTTGATTCTGAAGAAGCTGAAATATTCCAGAAGAAACTTGATGAGACCACCAGATTGCTCA
GGGAGCTAGCTCCAGGAAGCCCAGAATGAAAGTTTCAACACCAGACCCCCTCCCAACATGATCTGTCTCTTGGGTCCCTC
ATACAGAGAAATGCATCTCACTGAACAAGTGACCAATAATCTTAAAGAACTTGCACAGCGAGTAACTACAGGTGATATCA
TAAGCACATATGGAATTTGAAAAGCAATGGGGATTTCCATTCCTTCCCCTGTCATGGAAAACAACTCTGTGGATTTGACA
GAAGATACTGAAGAACCTAAAAAGACGAATGTTGCTGAATGTGGACCTGGTGGAAGT

Alignment

ORF - retro_ptro_2379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.56 %
• Parental protein coverage: 72.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQSIDFMADL
          MKEKIKNNDYQSIE.LKD.FKLMCTNAMIYNKPETIYYKAAKK.LHSGMKIL..ERIQSLKQSIDFMADL
Retrocopy MKEKIKNNDYQSIEKLKDIFKLMCTNAMIYNKPETIYYKAAKKRLHSGMKILRHERIQSLKQSIDFMADL

Parental  QKTRKQKDGTDTSQSGEDGGCWQR-EREDSGDVEAHAFKSPSKENKKKDKDMLEDKFKSNNLEREQEQLD
          QKT.KQ.D.TDTSQSGED.GCW.R..REDSGD..AHAFKSPSKENKKKDKDMLE.KFKSNNLER.Q.QLD
Retrocopy QKTQKQEDRTDTSQSGEDRGCWPR<KREDSGDAKAHAFKSPSKENKKKDKDMLEGKFKSNNLERAQGQLD

Parental  RIVKESGGKLTRRLVNSQCEFERRKPDGTTTLGLLHPVDPIVGEPGYCPVRLGMTTGRLQSGVNTLQGFK
          .IVKESGGKLTRRLVNSQC..ERRKPDGTT.LGLLHPVD.IVGEPGYCPVRLGMTTGRLQSGVNTLQGFK
Retrocopy GIVKESGGKLTRRLVNSQCKLERRKPDGTTMLGLLHPVDLIVGEPGYCPVRLGMTTGRLQSGVNTLQGFK

Parental  EDKR-NKVTPVLYLNYGPYSSYAPHYDSTFANISKDDSDLIYSTYGEDSDLPSDFSIHEFLATCQDYPYV
          EDKR.NKVTPVLYLNYGPYSSYAPHYDS..ANI.K.DSDLIYSTYGED.DLPSD.S.HEFLATCQDYP.V
Retrocopy EDKR<NKVTPVLYLNYGPYSSYAPHYDSIYANINKNDSDLIYSTYGEDTDLPSDLSSHEFLATCQDYPSV

Parental  MADSLLDVLTKGGHSRTLQEMEMSLPEG-EGHTRTLDTAKEMEQITEVEPPGRLDSST-QDRLIALKAVT
          MADSLLDVLTKGGHSRTLQE..MSLPE..EGHTRT.DTAKEME.ITEVEPPG.LDS.T.QDRLIALKAVT
Retrocopy MADSLLDVLTKGGHSRTLQEI*MSLPED>EGHTRTPDTAKEME-ITEVEPPGYLDSNT>QDRLIALKAVT

Parental  NFGVPVEVFDSEEAEIFQKKLDETTRLLRELQEAQNE-RLSTRPPPNMICLLG-PSYREMHLAEQVTSNL
          NFGVPV.VFDSEEAEIFQKKLDETTRLLREL.....E.......P......LG.PSYREMHL.EQVT.NL
Retrocopy NFGVPVKVFDSEEAEIFQKKLDETTRLLRELAPGSPE*KFQHQTPSQHDLSLG>PSYREMHLTEQVTNNL

Parental  KELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEEPKKTDVAECGPGGS
          KELAQ.VT.GDI.STYG..KAMGISIPSPVMENN.VDLTEDTEEPKKT.VAECGPGGS
Retrocopy KELAQRVTTGDIISTYGI*KAMGISIPSPVMENNSVDLTEDTEEPKKTNVAECGPGGS

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	0.09 RPM	21.81 RPM
SRP007412_cerebellum	0.25 RPM	31.91 RPM
SRP007412_heart	0.00 RPM	26.49 RPM
SRP007412_kidney	0.03 RPM	33.21 RPM
SRP007412_liver	0.00 RPM	17.48 RPM
SRP007412_testis	0.32 RPM	74.30 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2379 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2379 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3507
Gorilla gorilla	retro_ggor_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,