RetrogeneDB ID: retro_ggor_1895

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:160891079..160892773(+)
• 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_1895
AGAGTTAAGGAGGATAAAAAGAAGCGAGATCGAGACCGGGTGGAGAATGAGGCAGAAAAAGACCTCCAGTGTCACGCCCC
TGTGAGATTAGACTTGCCCCCGAGAAGCCTCTCACAAGCTCTTTAGCCAAACAAGAAGTAGAACAGACACCCCTTCAAGA
AGCTTTGAATCAACTGATGAGACAATTGTAGAGAAAAGATCCAAGTGCTTTCTTTTCATTTCCTGTGACTGATTTTATTG
CTCCTGGCTACTCCATGATCATTAAACACCCAATGGATTTTAGTACCATGAAACAAAAGATCAAGAACAATGACTATCAG
TCCATAGAAGAACTGAAGGATAACTTCAAACTAATGTGTACTAATGCCATGATTTACAATAAACCAGAGACCATTTATTA
TAAAGCTGCAAAGAAGCTGTTGCACTCAGGGATGAAAATTCTTAGCCAGGAAAGAATTCAGAGCCTGAAGCAGAGCATAG
ACTTCATGGCTGACTTGCAGAAAACTCGAAAGCAGAAAGATGGAACAGACACCTCACAGAGTGGGGAGGACAGAGGCTGC
TGGCAGAGAGAGAGAGAGGACTCTGGAGATGCCGAAGCACACGCCTTCAAGAGTCCCAGCAAAGAAAAAGAAAGACAAAG
ATACGCTTGAAGATAAGTTTAAAAGCAATAATTTAGAGAGAGAGCAGGAGCAGCTTGACCGCATTGTGAAGGAATCTGGA
GGAAAACTGACAAGGCGGCTTGTGAACAGTCAGTGCGAATTTGAAAGAAGAAAACCAGATGGAACAACGACGTTGGGACT
TCTCCATCCTGTGGATCCCATTGTAGGAGAGCCAGGCTACTGCCCTGTGAGACTGGGAATGACAACTGGAAGACTTCAGT
CTGGAGTGAATACTTTGCAGGGGTTCAAAGAGGATAAAAGGAACAAAGTCACTCCAGTGTTATATTTGAATTATGGGCCC
TACGGTTCTTATGCACCGCATTATGACTCCACATTTGCGAATATCAGCAAGGATGATTCTGATTTAATCTATTCAACCTA
TGGGGAAGACTCTGATCTTCCAAGCGATTTCAGCATCCATGAGTTTTTGGCCACGTGCCAAGATTATCCGTATGCCATGG
CAGATAGTTTACTGGATGTTTTAACAAAAGGAGGGCATTCCAGGACCCTACAAGAGATGGAGATGTCATTGCCTGAAGAT
GAAGGCCATACTAAGACACTTGACACAGCAAAAGAAATGGAGATTACAGAAGGAGAGCTGCCAGGGCGTTGGAGTCCAAT
ACTCAAGACAGGCTCATAGCGCTGAAAGCAGTAACAAATTTTGGCGTTCCAGTTGAAGTTTTTGACTCTGAAGAAGCTCA
AATATTCCAGAAGAAACTTGATGAGACCACCAGATTGCTCAGGGAACTCCAGGAAGCCCAGAATGAACGTTTGAGCACCA
GACCCCCTCCCAACATGATCTGTCTCTTGGGTCCCTCATACAGAGAAATGCATCTTGCTGAACAAGTGACCAATAATCTT
AAAGAACTTGCACAGCAAGTAACTCCAGGTGATATCGTAAGCACGTATGGAGTTCGAAAAGCAATGGGGATTTCCATTCC
TTCCCCCGTCATGGAAAACAACTTTGTGGATTTGACAGAAGACACTGAAGATCCTAAAAAGACGGATGTTGCTGAGTGTG
GACCTGGTGGAAGT

Alignment

ORF - retro_ggor_1895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.93 %
• Parental protein coverage: 87.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RVKEDKKKRDRDRVENEAEKDLQCHAPVRLDLPP-EKPLTSSLAKQEEVEQTPLQEALNQLMRQLQRKDP
          RVKEDKKKRDRDRVENEAEKDLQCHAPVRLDLPP.EKPLTSSLAKQE.VEQTPLQEALNQLMRQL.RKDP
Retrocopy RVKEDKKKRDRDRVENEAEKDLQCHAPVRLDLPP<EKPLTSSLAKQE-VEQTPLQEALNQLMRQL*RKDP

Parental  SAFFSFPVTDFIAPGYSMIIKHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAK
          SAFFSFPVTDFIAPGYSMIIKHPMDFSTMK.KIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAK
Retrocopy SAFFSFPVTDFIAPGYSMIIKHPMDFSTMKQKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAK

Parental  KLLHSGMKILSQERIQSLKQSIDFMADLQKTRKQKDGTDTSQSGEDGGCWQREREDSGDAEARAFKS-PS
          KLLHSGMKILSQERIQSLKQSIDFMADLQKTRKQKDGTDTSQSGED.GCW.....DSGDAEA.AFKS.P.
Retrocopy KLLHSGMKILSQERIQSLKQSIDFMADLQKTRKQKDGTDTSQSGEDRGCWXXXXXDSGDAEAHAFKS>PA

Parental  KENKKKDKDMLEDKFKSNNLEREQEQLDRIVKESGGKLTRRLVNSQCEFERRKPDGTTTLGLLHPVDPIV
          K..KKKDKD.LEDKFKSNNLEREQEQLDRIVKESGGKLTRRLVNSQCEFERRKPDGTTTLGLLHPVDPIV
Retrocopy K--KKKDKDTLEDKFKSNNLEREQEQLDRIVKESGGKLTRRLVNSQCEFERRKPDGTTTLGLLHPVDPIV

Parental  GEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPYSSYAPHYDSTFANISKDDSDLIYS
          GEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPY.SYAPHYDSTFANISKDDSDLIYS
Retrocopy GEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPYGSYAPHYDSTFANISKDDSDLIYS

Parental  TYGEDSDLPSDFSIHEFLATCQDYPYVMADSLLDVLTKGGHSRTLQEMEMSLPEDESHTRTLDTAKEMEQ
          TYGEDSDLPSDFSIHEFLATCQDYPY.MADSLLDVLTKGGHSRTLQEMEMSLPEDE.HT.TLDTAKEME.
Retrocopy TYGEDSDLPSDFSIHEFLATCQDYPYAMADSLLDVLTKGGHSRTLQEMEMSLPEDEGHTKTLDTAKEME-

Parental  ITEVEPPGH-LDSSTQDRLIALKAVTNFGVPVEVFDSEEAEIFQKKLDETTRLLRELQEAQNERLSTRPP
          ITE.E.PG..L.S.TQDRLIALKAVTNFGVPVEVFDSEEA.IFQKKLDETTRLLRELQEAQNERLSTRPP
Retrocopy ITEGELPGR<LESNTQDRLIALKAVTNFGVPVEVFDSEEAQIFQKKLDETTRLLRELQEAQNERLSTRPP

Parental  PNMICLLGPSYREMHLAEQVTNNLKELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEEPK
          PNMICLLGPSYREMHLAEQVTNNLKELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTE.PK
Retrocopy PNMICLLGPSYREMHLAEQVTNNLKELAQQVTPGDIVSTYGVRKAMGISIPSPVMENNFVDLTEDTEDPK

Parental  KTDVAECGPGGS
          KTDVAECGPGGS
Retrocopy KTDVAECGPGGS

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	0.62 RPM	25.85 RPM
SRP007412_cerebellum	0.91 RPM	28.56 RPM
SRP007412_heart	0.09 RPM	8.66 RPM
SRP007412_kidney	0.53 RPM	30.09 RPM
SRP007412_liver	0.26 RPM	14.38 RPM
SRP007412_testis	1.86 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_1895 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1895 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2723
Pan troglodytes	retro_ptro_1840

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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,