RetrogeneDB ID: retro_ptro_2610

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:26076777..26077863(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC86
• Ensembl ID: ENSPTRG00000003721
• Aliases: None
• Description: Pan troglodytes coiled-coil domain containing 86 (CCDC86), mRNA. [Source:RefSeq mRNA;Acc:NM_001246553]

Sequence

>retro_ptro_2610
ATGGATACACCGCCAAGGCGAAGCCGACAGCTGGAAGGCCTAGGGCCTGAATCCCTCCAGAGCCTCACCTCAGTTTCGCA
GTAGGAGATGGGTCCTTGTGGAGTTCGAGTTAGACACAGAAGAAACGAGGGAGCCCGGGTCTCCTCCGAGTGTGCAACAA
GCTGGCCTGGGCCCCCCCCCCCCCGAAAGGAGGCTGGAGAGAAGCCCAGGATCACCCAGTCTTTGCAGCAGGGTGCAGGC
TTGGAGTCCCCCCAAGGGCGGCCAGAATCAGTTCCAGGGTCCCCCCAGTGTCAGCAAGGCCTACACCTGGAGTCGCCTCA
AAGGCAGCTGGAGTCCAGTCCTGAATCCCCACGATGTCAGCCGAAGCCAAGTGAGGAGGCACCCAAGTGTTCTCAGGGCC
AGGGAGTACCTGGCCTCGGAGTTGGCCCAAAGTAAGGAGGAGCTGATCCCAGGGGGCCCCCCAGCATCAGCTACTGCCGG
GGCCAGGATCACTAGAGCCTTAACCCCAGTCAGGAAGCTCCGGGTCCGGAGCCCTCTCAGCCACTACTGCAGCTAACACT
CGAGGCACCTGGCTTCCCCCAGGGTCAGCACGAGCAGAGCAAACTACCTCCAGCTGGGGAGATGGTGACAGACGGCTTCG
GGGCAAAGAAGCCAAAGGGTTCTTCATCCCAGGCCCCAGCGTCCAAGAAGCTGAAGGAGGAGCAGCTTCCTGTAATCCCG
AAGGGGAAGCCCAAATCGGGGCAAGTGTGGAAGGACCGCTCCAAGAAAAGATTCTCTCAGATGCTTTAGGACAAGCCCCT
GCGTATATCGTAGCAGCGGAAGATGAAGCAGGAGAGGAAGCTGGCCAAGGACTTTGCCCGTCACCTGGAGGAGGAGTAGG
AGAGGCGCCGCCAGGAGAAGAAACAGCGTCGGGCGGAGAACCTGAAATGCCGCCTGGAGAACGAGCAGAAGGTGGAGATC
GTCCAAGTGATCCGAAACCCTGCCAAGCTCAAGCGGGCAAAGCAGCAGCAGCTGCGCTCCATTGAGAAGCGGGACACCCT
AGCCCTGCTGCAGAAGCAGCCGACCTAGCGGCCGGCAGCCAAGATC

Alignment

ORF - retro_ptro_2610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MDTPLRRSRRLGGLRPESPESLTSVSR-TRRALVEFESNPEETREPGSPPSVQRAGL--GSPERPPKTSP
          MDTP.RRSR.L.GL.PES..SLTSVS...R..LVEFE...EETREPGSPPSVQ.AGL.....ER....SP
Retrocopy MDTPPRRSRQLEGLGPESLQSLTSVSQ>RRWVLVEFELDTEETREPGSPPSVQQAGLXXXXXERRLERSP

Parental  GSPRL-QQDAGLESPQG-QPEPGAASPQRQQDLHLESPQRQPEYSPESPRCQPKPSEEAPKCSQDQGV-L
          GSP.L.........P.G..PE....SPQ.QQ.LHLESPQRQ.E.SPESPRCQPKPSEEAPKCSQ.QGV.L
Retrocopy GSPSLCSRVQAWSPPKG<RPESVPGSPQCQQGLHLESPQRQLESSPESPRCQPKPSEEAPKCSQGQGV>L

Parental  ASELAQSKEELTP-GAPQHQLPPVPGSPEP-YPGQQAPGPEPSQPLLELTPRAPGSPRGQHEPSKPPPAG
          ASELAQSKEEL.P.GAPQHQL.P.PGS.EP..P.Q.APGPEPSQPLL.LT..APG.P.GQHE.SK.PPAG
Retrocopy ASELAQSKEELIP>GAPQHQLLPGPGSLEP>NPSQEAPGPEPSQPLLQLTLEAPGFPQGQHEQSKLPPAG

Parental  ETVTGGFGAKKRKGSSSQALASKTLNKEELPVIPKGKPKSGRVWKDRSKKRFSQMLQDKPLRTSWQRKMK
          E.VT.GFGAKK.KGSSSQA.ASK.L..E.LPVIPKGKPKSG.VWKDRSKKRFSQML.DKPLR.S.QRKMK
Retrocopy EMVTDGFGAKKPKGSSSQAPASKKLKEEQLPVIPKGKPKSGQVWKDRSKKRFSQML*DKPLRIS*QRKMK

Parental  ERQERKLAKDFARHLEEEKERRRQEKKQRRAENLKRRLENERKAEVVQVIRNPAKLKRAKKKQLRSIEKR
          ..QERKLAKDFARHLEEE.ERRRQEKKQRRAENLK.RLENE.K.E.VQVIRNPAKLKRAK..QLRSIEKR
Retrocopy --QERKLAKDFARHLEEE*ERRRQEKKQRRAENLKCRLENEQKVEIVQVIRNPAKLKRAKQQQLRSIEKR

Parental  DTLALLQKQPPQQPAAKI
          DTLALLQKQP...PAAKI
Retrocopy DTLALLQKQPT*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	10.03 RPM
SRP007412_cerebellum	0.00 RPM	11.69 RPM
SRP007412_heart	0.03 RPM	5.48 RPM
SRP007412_kidney	0.00 RPM	9.07 RPM
SRP007412_liver	0.00 RPM	10.05 RPM
SRP007412_testis	0.00 RPM	57.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2610 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2610 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2610 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3834
Gorilla gorilla	retro_ggor_2582
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 ,