RetrogeneDB ID: retro_ptro_2216

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:179976767..179977563(+)
• 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_2216
CAGCCAGAGCCAAGCCCAGGGTCCCCCGAGCATCAGCAAGATCTACACCTGGAGTCACCTCAAAGACAGCGAGAGTCTAG
CTCTGAATCCCCACAATGTCAGTCAAAGCCAAGTGAGGAGGCACCACGGTGTTCTCAGGGCCAGGGAGAACCAGCCTCCG
AGTGGGCCCAGAGTCCAGAGGAGCTGACCCGGGGGGTGGGGGTGGCATGAGCACCTATACCCGGGCCCAGGATCACCAGA
GCCTTACCCCAGTCAGCAGGGGCCGAGTTCAGAGCCGTCACGGCCAGTACGGGAGCTGACACCCGAGGCACCTGGCTCCC
CGCCGGGGTCAGCAGGAGCCAAGCAAGCTGCCTCTGGCTGGGGAGAGGTAACAGGCGGCCATGGGGCAAAGAAGGAAAAA
GGTTCTTCAGCCCAGGCTCCAGTATCCAAGAAGTCGAAGGAGGAGGAGGAGGAGTTTCCTATAATCCAGAAGGGGAGGCC
CACATTGGTGGGGGTGTGGAAAGACCACTGCAAGAAAAAGTTATCCCAGATGGTTCAGGACAAGCCCCTGCACACATCCT
GGCAGTGGAAGATGAAGGAACAGCAGGAAAGGAAGCTTGCCAAGGATTCTGCCCCTAACCTGGAGGAGGAGAAGGAAAGG
CACTGCCAGGAGAAGAAACAGCGCTGGGCCAAGAACCTGAAACATCACCTATAGAACGAGTGGAAGGCAGAGATTGTCCA
AGTGATCCAAAGCCCCACCAAGCTCAAGCTGGCGAGGACACAGCAGCTGTGCTCCACTGAGACACGGGACACCCTG

Alignment

ORF - retro_ptro_2216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.31 %
• Parental protein coverage: 72.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QPEPGAASPQRQQDLHLESPQRQPEYSPESPRCQPKPSEEAPKCSQDQGVLASELAQSKEELTPGAPQHQ
          QPEP...SP..QQDLHLESPQRQ.E.S.ESP.CQ.KPSEEAP.CSQ.QG..ASE.AQS.EELT.G.....
Retrocopy QPEPSPGSPEHQQDLHLESPQRQRESSSESPQCQSKPSEEAPRCSQGQGEPASEWAQSPEELTRGVGVA*

Parental  LPPVPG-SPEPYPGQQAPGP--EPSQPLLELTPRAPGSP-RGQHEPSKPPPAGE-TVTGGFGAKKRKGSS
          .P..PG....P.P.....GP..EPS.P..ELTP.APGSP.RGQ.EPSK.P.AGE..VTGG.GAKK.KGSS
Retrocopy AP-IPG>PGSPEPYPSQQGPSSEPSRPVRELTPEAPGSP>RGQQEPSKLPLAGE<EVTGGHGAKKEKGSS

Parental  SQALASKTL--NKEELPVIPKGKPKSGRVWKDRSKKRFSQMLQDKPLRTSWQRKMKERQERKLAKDFARH
          .QA..SK......EE.P.I.KG.P....VWKD..KK..SQM.QDKPL.TSWQ.KMKE.QERKLAKD.A..
Retrocopy AQAPVSKKSKEEEEEFPIIQKGRPTLVGVWKDHCKKKLSQMVQDKPLHTSWQWKMKEQQERKLAKDSAPN

Parental  LEEEKERRRQEKKQRRAENLKRRLENERKAEVVQVIRNPAKLKRAKKKQLRSIEKRDTL
          LEEEKER..QEKKQR.A.NLK..L.NE.KAE.VQVI..P.KLK.A...QL.S.E.RDTL
Retrocopy LEEEKERHCQEKKQRWAKNLKHHL*NEWKAEIVQVIQSPTKLKLARTQQLCSTETRDTL

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	0.00 RPM	5.48 RPM
SRP007412_kidney	0.00 RPM	9.07 RPM
SRP007412_liver	0.00 RPM	10.05 RPM
SRP007412_testis	0.21 RPM	57.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2216 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2216 has 0 orthologous retrocopies within eutheria group .

---

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,