RetrogeneDB ID: retro_mmul_2271

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:152490875..152491646(-)
• Located in intron of: ENSMMUG00000019898

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP2
• Ensembl ID: ENSMMUG00000001990
• Aliases: None
• Description: adenylyl cyclase-associated protein 2 [Source:RefSeq peptide;Acc:NP_001253461]

Sequence

>retro_mmul_2271
GTCTTAAAGGGCTACAAACACACGATTTACAGGGTGTGGATTGGGTGAGGTCATGTGAACATTTGGAGTGAGTTTCAAGC
ATGCATCAAGGAGCACCACACCACGGGCCTCTTGTGGAGCAGAACGGGTCCTGCAGCGCCCACATCAGCGCTTTCTGTTC
TCTCCTGAGGGCCTGACCTTTCTCCACATCCTCCTCCTCCACCTCCTCCAGGGCCCCTCCACTTTTTGAGAATGAAGACA
CAAAAGAAAAGTCCTCTCCTTCATGCTCAGCTTTATTTGCCCGGCTTAACCAAGGAGAAGCCTAACCTGGCAGAACCAGG
GCTCTGGCACGTCACAGATGACCAGAAGGTCTATACAAGAATCCCAGCCTGCAGGCTCACAGAGGGCAAACTGCATCTCT
CCCCAGAAGCCACACTCCAAGTCCCACATCTCCCAAACCTCATCCTTCCCAGACACATGCACCCGTGTTCAAGTTGGAAG
GAAGGAAATGGAGAGCAGAGTACCAAGAAGACACGAATGACCTTGTGATTTCAGAGACTGAGCTGAAACATGCGGCTTAC
ATTTTCAAATGTGAAAAATCAACTCTCCCGATGAAAGGGAAAGTAAACTCCACTCCAGTGAGTGGATAACCGTAAGAAGT
TTGGTCGGGTGTTTGATAGTGTGATGGGCATTGTGGAATCGACCAACTCCAAGGACATTCAAATCCAGGTAATGGGGAGA
GTACCAGCAATTTCCACTAATAAGACCGAAGGTTGCCATACATACCTAACT

Alignment

ORF - retro_mmul_2271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.94 %
• Parental protein coverage: 53.46 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLKDYKHSDLRHVDWVK-SYLNIWSELQAYIKEHHTTGLTWSKTGPVASTVSAFSVLSSGPGLPPPPPPP
          VLK.YKH...R...W......NIWSE.QA.IKEHHTTGL.WS.TGP.A.T.SA.SVLS.GP.L.P.PPPP
Retrocopy VLKGYKHTIYRV--WIG*GHVNIWSEFQACIKEHHTTGLLWSRTGPAAPT-SALSVLS*GPDLSPHPPPP

Parental  PPPGP-PPLFENEGKKEESSPSRSALFAQLNQGEA---ITKGLRHVTDDQKTYKNPSLRAQGGQTRSPTK
          PPPGP.PPLFENE..KE.SSPS.SALFA.LNQGEA....T..L.........YKNPSL.A..GQT.S...
Retrocopy PPPGP<PPLFENEDTKEKSSPSCSALFARLNQGEA*PGRTRALARHR*PEGLYKNPSLQAHRGQTASLPR

Parental  SHTPSPTSPKSHPSQKHAPVLELEGKKWRVEYQEDRNDLVISETELKQVAYIFKCEKSTLQI-KGKVNSI
          SHTPSPTSPK.HPSQ.HAPV..LEG.KWR.EYQED.NDLVISETELK..AYIFKCEKSTL...KGK....
Retrocopy SHTPSPTSPKPHPSQTHAPVFKLEGRKWRAEYQEDTNDLVISETELKHAAYIFKCEKSTLPM>KGK*TPL

Parental  I-IDNCKKLGLVFDNVVGIVEVINSQDIQIQVMGRVPTISINKTEGCHIYLS
          ...DN.KK.G.VFD.V.GIVE..NS.DIQIQVMGRVP.IS.NKTEGCH.YL.
Retrocopy Q*VDNRKKFGRVFDSVMGIVESTNSKDIQIQVMGRVPAISTNKTEGCHTYLT

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	0.00 RPM	205.84 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	167.07 RPM
SRP007412_cerebellum	1.16 RPM	71.03 RPM
SRP007412_heart	0.12 RPM	47.93 RPM
SRP007412_kidney	0.12 RPM	2.23 RPM
SRP007412_liver	0.20 RPM	0.36 RPM
SRP007412_testis	0.00 RPM	3.32 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2271 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2271 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1451
Pan troglodytes	retro_ptro_987

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 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	ENSPTRG00000017750	1 retrocopy	retro_ptro_987,