RetrogeneDB ID: retro_ptro_987

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:88783491..88784661(-)
• Located in intron of: ENSPTRG00000006614

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP2
• Ensembl ID: ENSPTRG00000017750
• Aliases: None
• Description: Adenylyl cyclase-associated protein [Source:UniProtKB/TrEMBL;Acc:H2QSC2]

Sequence

>retro_ptro_987
GCTTTCCTTCTGATGGCATCTCATGACCAACAACCCCGAGAGAATGCATGGCTGCATTTCTGAAACCCAAATCAGAAAAG
ATTCAGAAGTCCAAACCTTCAAAGAGAGAAACCGAGGGAGTAACATGTTTAGTCATCTCTCGGATGTCAGCAAAAGCCTC
CCTGCCCTTGGCTGCATAACTGTGTCCCCCAACTTGGGTACTTACGTCAACGAGATGTGTGATGCTGCCACCTTTTACAC
TAACAGGGTCTTAAAGGGCTACAAACATGATTTACACCGTGTGGATTGGGTGAGGTCATATGTGAACATTTGGAGTGAGT
TTCAAGCATGCGTCAAGGAGCACCACACCACGGGCCTCACGTGGAGCAGAACAGGTCCGCAGCACCCACGTCAGCGCTTT
CTGTTCTCTCCTGAGGGCCTGACCTTTCTCCACATCCTCCTCCTCCACCTCCTCCAGGGCCCCTCCACTTTTTGAGAATG
AGGACACAAAAGAAAAGTCCTCTCCTTCATGCTCAGCTTTATTTGCCCGGTTTAACCAGGGAGAAGCCTAACCCTGCAGA
ACCAGGGCTCTGGCACATCACTGATGACCAGAAGGCCTATATAAGAATCCCAGCCTGCAGGCTCACGGAGGGCAAAGTAC
GTCTCCCCACAAAAGCTACACTCCAAGTCCCACATCTCCCCAACCTCATCCTTCCCAGAAACATGCACCCGTGTTCAAGT
TGGAAGGAAGTAAATGGAGAGCAGAGTACCAAGAAGACAGGAATGACCTTGTGATTTCAGAGACTGAGCTGAAACAAGCG
GCTTACATTTTCAATTGTGAAAAATCAGCTCTCCCAATGAAAGGGAAAGTAAACTTCATTCCAGTGGAAAACTGTAAGAA
GTTTGGTCTGGTCTTTGACAGTGTGGTGGGCATTGGGGAAGTGACCAACTCCAAGTACATTCAAATCCAGGTAATGGGGA
GAGTACCAGCAATTTCCACTAATAAGACAGAAGGTTGCCACACATACCTAACTCGGGGAAGATGCATTAGACTGTGAGAT
TGTGAGCATCATATCATCCAAAATGAATATACTTATTCGTCAGGGTGGTAATGACAGAGAATTTCCTGTCCCTGAGCAGT
TCAAGACAGCATGGGATGGATCCAAGTTGGTCAGTGAACCCCCTCACCTG

Alignment

ORF - retro_ptro_987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.11 %
• Parental protein coverage: 81.55 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AFLLMASQYQQPHEND-VAALLKPISEKIQ-EIQTFRERNRGSNMFNHLSAVSESIPALGWIAVSPKPGP
          AFLLMAS..QQP.EN...AA.LKP.SEKIQ.E.QTF.ERNRGSNMF.HLS.VS.S.PALG.I.VSP..G.
Retrocopy AFLLMASHDQQPRENA<MAAFLKPKSEKIQ<EVQTFKERNRGSNMFSHLSDVSKSLPALGCITVSPNLGT

Parental  YVKEMNDAATFYTNRVLKDYKHSDLRHVDWVKSYLNIWSELQAYIKEHHTTGLTWSKTGP-VASTVSAFS
          YV.EM.DAATFYTNRVLK.YKH.DL..VDWV.SY.NIWSE.QA..KEHHTTGLTWS.TGP..A.T.SA.S
Retrocopy YVNEMCDAATFYTNRVLKGYKH-DLHRVDWVRSYVNIWSEFQACVKEHHTTGLTWSRTGP<AAPT-SALS

Parental  ALSSGPGLPPPPPPPPPPGP-PPLFENEGKKEESSPSRSALFAQLNQGEA---ITKGLRHVTDDQKTYKN
          .LS.GP.L.P.PPPPPPPGP.PPLFENE..KE.SSPS.SALFA..NQGEA....T..L.H.......YKN
Retrocopy VLS*GPDLSPHPPPPPPPGP<PPLFENEDTKEKSSPSCSALFARFNQGEA*PCRTRALAHH**PEGLYKN

Parental  PSLRAQGGQTQSPTKSHTPSPTSPKSYPSQKHAPVLELEGKKWRVEYQEDRNDLVISETELKQVAYIFKC
          PSL.A.GGQ..SP.KS.TPSPTSP...PSQKHAPV..LEG.KWR.EYQEDRNDLVISETELKQ.AYIF.C
Retrocopy PSLQAHGGQSTSPHKSYTPSPTSPQPHPSQKHAPVFKLEGSKWRAEYQEDRNDLVISETELKQAAYIFNC

Parental  EKSTLQIKGKVNSIIIDNCKKLGLVFDNVVGIVEVINSQDIQIQVMGRVPTISINKTEGCHIYLS-GD-A
          EKS.L..KGKVN.I...NCKK.GLVFD.VVGI.EV.NS..IQIQVMGRVP.IS.NKTEGCH.YL..G..A
Retrocopy EKSALPMKGKVNFIPVENCKKFGLVFDSVVGIGEVTNSKYIQIQVMGRVPAISTNKTEGCHTYLT>GEDA

Parental  LDCEIVSAKSSEMNILIPQDGDYREFPIPEQFKTAWDGSKLITEPAEI
          LDCEIVS..SS.MNILI.Q.G..REFP.PEQFKTAWDGSKL..EP...
Retrocopy LDCEIVSIISSKMNILIRQGGNDREFPVPEQFKTAWDGSKLVSEPPHL

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	0.09 RPM	85.15 RPM
SRP007412_cerebellum	0.47 RPM	40.94 RPM
SRP007412_heart	0.15 RPM	78.43 RPM
SRP007412_kidney	0.10 RPM	16.48 RPM
SRP007412_liver	0.10 RPM	9.36 RPM
SRP007412_testis	0.42 RPM	0.74 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_987 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_987 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1451
Macaca mulatta	retro_mmul_2271

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009977	1 retrocopy	retro_cfam_1385,
Cavia porcellus	ENSCPOG00000008839	1 retrocopy	retro_cpor_1367,
Homo sapiens	ENSG00000112186	1 retrocopy	retro_hsap_1451,
Macaca mulatta	ENSMMUG00000001990	1 retrocopy	retro_mmul_2271,
Pan troglodytes	ENSPTRG00000000583	2 retrocopies	retro_ptro_1796, retro_ptro_484,
Pan troglodytes	ENSPTRG00000017750	1 retrocopy	retro_ptro_987 ,