RetrogeneDB ID: retro_ggor_2372

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:111574449..111575866(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRD7
• Ensembl ID: ENSGGOG00000014824
• Aliases: None
• Description: None

Sequence

>retro_ggor_2372
ATGAAAGAAAAGATCAAGAACAATGACTACCAGTCCATAGAAAAACTAAAGGATATTTTCAAACTAATGTGTACTAATGC
CATGATTTACAATAAACCAGAGACCATTTATTATAAAGCTGCAAAGAAGCGGTTGCACTCGGGGATGAAAATTCTTAGAC
ATGAAAGAATTCAGAGCCTGAAGCAGAGCATAGACTTCATGGCTGATTTGCAGAAAACTCAAAAGCAGGAAGACAGAACA
GACACCTCACAGAGTGGGGAGGACAGAGGCTGCTGGCCGAGAAGAGAGAGGACTCTGGAGATGCCAAAGCACACGCCTTC
AAGAGTCCCAGCAAAAAAAATAAAAAGAAAGACAAAGACATGCTTGAAGATAAGTTTAAAAGCAATAATTTAGAGAGAGC
GCAGGAGCAGCTTGATCGCATCGTGAAGGAATCTGGAGGAAAGCTGACCAGGCGGCTTGTGAACAGTCAGTGCAAATTGG
AAAGAAGAAAACCAGACGGAACAACAATGTTGGGACTTCTCCATCCTGTGGATCTCATTGTAGGAGAGCCAGGCTACTGC
CCTGTGAGACTGGGAATGTCAACTGGAAGACTTCAGTCTGGTGTGAATACTTTGCAGGGGTTCAAAGAGGACAAAAGAAC
AAAGTCACTCCAGTGTTATATTTGAATTACGGGCCCTACAGTTCTTATGCACCGCATTATGACTCCACATATGCAAATAT
CAACAAGAATGATTCTGATTTAATCTATTCAACCTATGGGGAAGACACAGATCTTCCAAGCGATCTCAGCAGCCATGAGT
TTTTGGCCACGTGCCAAGATTATCCATCTGTGATGGCAGATAGTTTACTGGATGTTTTAACAAAAGGAGGGCATTCCAGG
ACCCTACAAGAGATTTAGATGTCACTGCCTGAAGATGGAAGGCCATACTAGGACACCTGACACAGCAAAAGAAATGGAGA
TTACAGAAGTAGAGCCACCAGGATGTCTGGACTCCAATACTTCAATACAGGCTCATAGCGCTGAAAGCAGTAGCAAACTT
TGGCGTTCCGGTTGAAGTTTTTGATTCTGAAGAAGCTGAACTATTCCAGAAGAAACTTGATGAGACCACCAGACTGCTCA
GGGAGCTAGCTCCAGGAAGCCCAGAATGAATGTTTCAACACCAGACCCCCTCCCAACATGATCTGTCTCTTGGGTCCCTC
ATACAGAGAAATGCATCTCACTGAAAAAGTGACCAGTAATCTTAAAGAACTTGCACAGCAAGTAACTACAGGTGATATCG
TAAGCACATATGGAGATTGAAAAGCAATGGGGATTTCTATTCCTTCTCCCGTCATGGAAAACAACTCTGTGGATTTGACA
GAAGATACTGAAGAACCTAAAAAGACGAATGTTGCTGAATGTGGACCTGGTGGAAGT

Alignment

ORF - retro_ggor_2372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.15 %
• 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-EREDSGDAEARAFKSPSKENKKKDKDMLEDKFKSNNLEREQEQLD
          QKT.KQ.D.TDTSQSGED.GCW.R..REDSGDA.A.AFKSPS.....KDKDMLEDKFKSNNLER.QEQLD
Retrocopy QKTQKQEDRTDTSQSGEDRGCWPR<KREDSGDAKAHAFKSPSXXXXXKDKDMLEDKFKSNNLERAQEQLD

Parental  RIVKESGGKLTRRLVNSQCEFERRKPDGTTTLGLLHPVDPIVGEPGYCPVRLGMTTGRLQSGVNTLQGFK
          RIVKESGGKLTRRLVNSQC..ERRKPDGTT.LGLLHPVD.IVGEPGYCPVRLGM.TGRLQSGVNTLQGFK
Retrocopy RIVKESGGKLTRRLVNSQCKLERRKPDGTTMLGLLHPVDLIVGEPGYCPVRLGMSTGRLQSGVNTLQGFK

Parental  EDKR-NKVTPVLYLNYGPYSSYAPHYDSTFANISKDDSDLIYSTYGEDSDLPSDFSIHEFLATCQDYPYV
          EDKR.NKVTPVLYLNYGPYSSYAPHYDST.ANI.K.DSDLIYSTYGED.DLPSD.S.HEFLATCQDYP.V
Retrocopy EDKR<NKVTPVLYLNYGPYSSYAPHYDSTYANINKNDSDLIYSTYGEDTDLPSDLSSHEFLATCQDYPSV

Parental  MADSLLDVLTKGGHSRTLQEMEMSLPED-ESHTRTLDTAKEMEQITEVEPPGHLDSST-QDRLIALKAVT
          MADSLLDVLTKGGHSRTLQE..MSLPED.E.HTRT.DTAKEME.ITEVEPPG.LDS.T.Q.RLIALKAV.
Retrocopy MADSLLDVLTKGGHSRTLQEI*MSLPED>EGHTRTPDTAKEME-ITEVEPPGCLDSNT>QYRLIALKAVA

Parental  NFGVPVEVFDSEEAEIFQKKLDETTRLLRELQEAQNERLSTRPPPNMICL-LG-PSYREMHLAEQVTNNL
          NFGVPVEVFDSEEAE.FQKKLDETTRLLREL.....E.......P....L.LG.PSYREMHL.E.VT.NL
Retrocopy NFGVPVEVFDSEEAELFQKKLDETTRLLRELAPGSPE*MFQHQTPSQHDLSLG>PSYREMHLTEKVTSNL

Parental  KELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEEPKKTDVAECGPGGS
          KELAQQVT.GDIVSTYG..KAMGISIPSPVMENN.VDLTEDTEEPKKT.VAECGPGGS
Retrocopy KELAQQVTTGDIVSTYGD*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	0.10 RPM	25.85 RPM
SRP007412_cerebellum	0.04 RPM	28.56 RPM
SRP007412_heart	0.09 RPM	8.66 RPM
SRP007412_kidney	0.20 RPM	30.09 RPM
SRP007412_liver	0.08 RPM	14.38 RPM
SRP007412_testis	0.10 RPM	78.01 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2372 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2372 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3507
Pan troglodytes	retro_ptro_2379

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 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,