RetrogeneDB ID: retro_mmul_2294

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:76159322..76160097(+)
• Located in intron of: ENSMMUG00000021588

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAX1
• Ensembl ID: ENSMMUG00000000543
• Aliases: None
• Description: None

Sequence

>retro_mmul_2294
ATACGTCCCTCCTCCTCCCCACCTCGTGGCAGCAGCAGCCCTCTAGCTTTGGCTCCGTGGACTGGCTCTCCCAAAACAGC
TGCTCAGGACCGACCCACACCCCCAGGCCTGCCAACGTCTCCCTGAGGAGCCTCCCCGGCCCAGGTCAGGCATCCGGCTC
CTAGGAGCCCCCTCAGGCCGTCAGCATCACAGAGGCTAGGTCCTCAAACCTGCCTCCGTGGGAGAGGACCGTGGCTGGGT
AAAGGGCCAAACACCTGGCGGGCTCCCTGGCGTCCCCACAGTCTTCACCATGGAGCAGGTCCGCGCCTTGGAGGGCGTCT
TCCGGCAAGACCAGTACCTGGGCCCTCTGCAGCGGAAGAGGCTGGCCAGGGAGATGCAGCTGTCAGAGGTCCAGATAAAA
ACCTGGTTTCAAAATCGCCGGATAAAACACAAACGGCAAATGCAGGACTCCCAGCTGAACAGCCCCTTCTCGGGGGTCAC
TCCACACACCCCCGGCTTTCCACTCACCGTCTTCTGGCCTTGCCAATGGCCCGCGGCTGCTGTGCCCTTAGGCACCACTA
CCTGGGCCCCAGGTTCCGATGCTGCCCCCTGGCTCCTTCTGGGATCTCTGCCAAGTGGAACAAGAGGCCCTGGCCTCTGA
GTGGGCTTCCTGCTGAGGGCAGCCTCTGGCCTACCACCCTGCAAAGCCCAGGAAGTGGCATGCATACGCTGGGACCAGCC
CTGTCCACGGGACCCTGGGGCCTGGTGTGCTCTGCTGGAGACAGGGGACGCATTT

Alignment

ORF - retro_mmul_2294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MRLSSSPPRG-QQQPSSFGSVDWLSQSSCSGLT-PSPRPADVSPGSLPGPGQISGAR-EPPQAISIKEAE
          .R.SSSPPRG.QQQPSSFGSVDWLSQ.SCSG.T.P.P......P...P.P...SG.R..P..........
Retrocopy IRPSSSPPRG<QQQPSSFGSVDWLSQNSCSGPT<PHPQACQRLPEEPPRPR--SGIR<APRSPLRPSASQ

Parental  RASWEPASEASMPGLSKEPNTLRGP-RVRTAFTTEQVRTLEGVFQHHQYLSPLERKRLAREMQLSEVQIK
          R...........P.L.K.PNT.R.P..V.T.FT.EQVR.LEGVF...QYL.PL.RKRLAREMQLSEVQIK
Retrocopy RLGPQTCLRGRGPWLGKGPNTWRAP>GVPTVFTMEQVRALEGVFRQDQYLGPLQRKRLAREMQLSEVQIK

Parental  TWFQNRRMKHKRQMQEVPPNSPFLG-SLHVPPAFHSPSSGLANGLQLLCPWAPLPGPQALMLPPGSFWGL
          TWFQNRR.KHKRQMQ....NSPF.G.SLH.PPAFHSPSSGLANG..LLCP.APLPGPQ..MLPPGSFW.L
Retrocopy TWFQNRRIKHKRQMQDSQLNSPFSG>SLHTPPAFHSPSSGLANGPRLLCP*APLPGPQVPMLPPGSFWDL

Parental  CQVEQEALASTGASCCRQPLAHHP-PTTGSGLPAPGPALSTGPWGL-CALPETGDAF
          CQVEQEALAS..ASC..QPLA.HP....GSG....GPALSTGPWGL.CAL.ETGDAF
Retrocopy CQVEQEALASEWASC*GQPLAYHP>QSPGSGMHTLGPALSTGPWGL>CALLETGDAF

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.06 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.04 RPM	0.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2294 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2294 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3973
Pan troglodytes	retro_ptro_2698

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151650	4 retrocopies	retro_hsap_1027, retro_hsap_2612, retro_hsap_3973, retro_hsap_4038,
Gorilla gorilla	ENSGGOG00000003340	3 retrocopies	retro_ggor_1830, retro_ggor_2668, retro_ggor_2708,
Macaca mulatta	ENSMMUG00000000543	2 retrocopies	retro_mmul_1477, retro_mmul_2294 ,
Nomascus leucogenys	ENSNLEG00000002047	5 retrocopies	retro_nleu_2033, retro_nleu_2054, retro_nleu_635, retro_nleu_664, retro_nleu_905,
Pan troglodytes	ENSPTRG00000003087	4 retrocopies	retro_ptro_1761, retro_ptro_2698, retro_ptro_2736, retro_ptro_702,