RetrogeneDB ID: retro_ggor_2582

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:27746489..27747570(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC86
• Ensembl ID: ENSGGOG00000013670
• Aliases: None
• Description: None

Sequence

>retro_ggor_2582
ATGGATACACCGCCAAGGCGAAGCTGACAGCTGGAAGGCCTAGGGCCTGAATCCCCCCAGAGCCTTACCTCAGTTTCGCG
TAGGAGATGGGTCCTTGTGGAGTTCGAGTTGGACCCAGAAGAAACGAGGGAGCCTGGGTCTCCTCCGAGTGTGCAACAAG
CTGGCCTGGGGCCCCCTGAAAGGACGCTGGAGAGAAGCCCAGGATCACCCAGTCTTTGCAGCAGGGTGCAGGCTTGGAGT
CCCCCCCAAGGGCGGCCAGAATCAGGTCCAGGGTCCCCCCAGTGTCAGCAAGGCCTACACCTGGAGTCGCCTCAAAGACA
GCTGGAGTCCAGTCCTCAATCCCCACGATGTCAGCCGAAGCCAAGTGAGGAGAAACCCAAGTGTTCTCAGGGCCAGGGAG
TACCTGGCCTCGGAGTTGGCCCAAAGTAAGGAGGAGCTGATCCCAGGGGCCCCCCCAGCACCAGCTACTGCCCAGGCCCA
GGATCACCAGAGCCTTAACCCCAGTCAGGAAGCTCCGGGTCCGGAGCCCTCTCAGCCACTACTGCAGCTAACACTTGAGG
CACCTGGCTTCCCCCAGGGTCAGCACGAGCAGAGCAAACCACCTCCAGCTGGGGAGATGGTGACAGACGGCTTCGGGGCA
AAGAAGCCAAAGGGTTCTTCATCCCAGGCCCCAGCGTCCAAGAAGCTGAAGGAGGAGCAGCTTCCTGTAATCCCGAAGGG
GAAGCCCAAATCAGGGCAAGTGTGGAAGGACCGCTCCAAGAAAAGATTCTCTCAGATGCTTCAGGACAAGCTCCTGCGTA
TATCGTGGCAGCGGAAGATGAAGCAGGAGAGGAAGCTGGCCAAGGACTTTGCCCGTCACCTGGAGGAGAAGTAGGAGAGG
CGCCGCCAGGAGAAGAAACAGCGTCGGGCGGAGAACCTGAAATGCCGCCTGGAGAACGAGCGGAAGGTGGAGATCGTCCA
AGTGATCCGAAACCCTGCCAAGCTCAAGGGGGCAAAGCAGCAGCAGCTGCGCTCCATTGAGAAGCGGGACACCCTAGCCC
TGCTGCAGAAGCAGCCGCCCTAGCGGCCGGCAGCCAAGATC

Alignment

ORF - retro_ggor_2582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.47 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MDTPLRRSRRLGGLRPESPESLTSVSRTRRALVEFESNPEETREPGSPPSVQRAGL-GSPERPPKTSPG-
          MDTP.RRS..L.GL.PESP.SLTSVSR.R..LVEFE..PEETREPGSPPSVQ.AGL.G.P.......P..
Retrocopy MDTPPRRS*QLEGLGPESPQSLTSVSRRRWVLVEFELDPEETREPGSPPSVQQAGL<GAP*KDAGEKPRI

Parental  SPRLQQDAGLEFP-QGQPEPGAASPQRQQDLHLESPQRQPEYSPESPRCQPKPSEEAPKCSQDQGV-LAS
          ...LQQ.AGLE.P.QG.PE.G..SPQ.QQ.LHLESPQRQ.E.SP.SPRCQPKPSEE.PKCSQ.QGV.LAS
Retrocopy TQSLQQGAGLESP>QGRPESGPGSPQCQQGLHLESPQRQLESSPQSPRCQPKPSEEKPKCSQGQGV>LAS

Parental  ELAQSKEELTPGAP-QHQLPPVP-GSPEP-YPGQQASGPEPSQPLLELTPRAPGSPRGQHEPSKPPPAGE
          ELAQSKEEL.PGAP.QHQL.P.P.GSPEP..P.Q.A.GPEPSQPLL.LT..APG.P.GQHE.SKPPPAGE
Retrocopy ELAQSKEELIPGAP>QHQLLPRP>GSPEP>NPSQEAPGPEPSQPLLQLTLEAPGFPQGQHEQSKPPPAGE

Parental  TVTGGFGAKKRKGSSSQALASKKLNKEELPVIPKGKPKSGRVWKDRSKKRFSQMLQDKPLRTSWQRKMKE
          .VT.GFGAKK.KGSSSQA.ASKKL..E.LPVIPKGKPKSG.VWKDRSKKRFSQMLQDK.LR.SWQRKMK.
Retrocopy MVTDGFGAKKPKGSSSQAPASKKLKEEQLPVIPKGKPKSGQVWKDRSKKRFSQMLQDKLLRISWQRKMK-

Parental  RQERKLAKDFARHLEEEKERRRQEKKQRRAENLKRRLENERKAEVVQVIRNPAKLKRAKKKQLRSIEKRD
          .QERKLAKDFARHLEE..ERRRQEKKQRRAENLK.RLENERK.E.VQVIRNPAKLK.AK..QLRSIEKRD
Retrocopy -QERKLAKDFARHLEEK*ERRRQEKKQRRAENLKCRLENERKVEIVQVIRNPAKLKGAKQQQLRSIEKRD

Parental  TLALLQKQPPQQPAAKI
          TLALLQKQPP..PAAKI
Retrocopy TLALLQKQPP*RPAAKI

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	0.00 RPM	9.73 RPM
SRP007412_cerebellum	0.00 RPM	5.16 RPM
SRP007412_heart	0.00 RPM	4.57 RPM
SRP007412_kidney	0.00 RPM	7.20 RPM
SRP007412_liver	0.00 RPM	3.80 RPM
SRP007412_testis	0.00 RPM	43.41 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_2582 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2582 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3834
Pan troglodytes	retro_ptro_2610
Macaca mulatta	retro_mmul_1622

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110104	2 retrocopies	retro_hsap_3276, retro_hsap_3834,
Gorilla gorilla	ENSGGOG00000013670	1 retrocopy	retro_ggor_2582 ,
Macaca mulatta	ENSMMUG00000000019	1 retrocopy	retro_mmul_1622,
Nomascus leucogenys	ENSNLEG00000013582	1 retrocopy	retro_nleu_2131,
Pongo abelii	ENSPPYG00000003205	1 retrocopy	retro_pabe_2818,
Pan troglodytes	ENSPTRG00000003721	2 retrocopies	retro_ptro_2216, retro_ptro_2610,