RetrogeneDB ID: retro_mmul_611

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:58292483..58293304(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTCN1
• Ensembl ID: ENSMMUG00000016964
• Aliases: None
• Description: V-set domain containing T cell activation inhibitor 1 [Source:HGNC Symbol;Acc:28873]

Sequence

>retro_mmul_611
TTCCAGAGTATAATTAGCATCATCATCATTCTGGCTGGAACACCTACACTCATCATTCGCTCTGGTATTTCAGGGAGACA
CTCCATCACAGTCACTACTCTCACCCCAGCTGGGAACACTGGGTAGGATGGAATCCTGAGCTGCACTTTTGAACTTGACA
TCAAACTTTCTGATATTGTGATACAATGGCTGATGGAAGGGGTTATAGGCTTTGTCCATGAGTTCAAAGAAGGCAAAGAT
GAGCTGTCAGAGCAGGATGAAATGTTCAGAGGCCTGATAGCAATGCTTGCTGATCAAGTGATAGTTGGCAATGCCTCTCT
GCGGCTGAAAAACATACAACTCACAGATGCTGGCACCTACAAATGTTATATCATCACTTCTAAAGGCAAGGGAATGCTAA
CCTTGCATATAAAACTGGAGCCTTCAGCATGCCAGAGGTGAAAGTAGACTATAATGCCAGCTCAGAGACCTTGCAATGTG
AGGCTCCCTGATGGTACCCCCGGACTACAGTGGTCTGAAGATCCCTAGTTGACTAGGGAGCCAAATTCTCGGAAGTCTCC
AATACCATCTTTGAGCTGAACTCTGAGAATGTGACCATGAAGGTTGTGTCTGTGCTCTACGATGTTATGATCAACAACAC
GTACTCCTGTATGATTGAAAATGACATTACCAAAGCAACGGGAGATATCAAAGCGACAGAATCTGAGATCAAAAGGTAGA
GCCACCTACAGCTGCTGAACCCAAAGCCTTCTCTGTGTATCTCTTCTTTTTTTGCCATCAGTTGGGCACTTCTGCCTCTC
GCCCCTTACCTCATGCTAAAA

Alignment

ORF - retro_mmul_611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.36 %
• Parental protein coverage: 97.16 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FWSIISIIFILAGAIALIIGFGISGRHSITVTTVASAGNIGEDGILSCTFEPDIKLSDIVIQWLKEGVIG
          F.SIISII.ILAG...LII..GISGRHSITVTT...AGN.G.DGILSCTFE.DIKLSDIVIQWL.EGVIG
Retrocopy FQSIISIIIILAGTPTLIIRSGISGRHSITVTTLTPAGNTG*DGILSCTFELDIKLSDIVIQWLMEGVIG

Parental  LVHEFKEGKDELSEQDEMFRGRTAVFADQVIVGNASLRLKNVQLTDAGTYKCYIITSKGKG-NANLEYKT
          .VHEFKEGKDELSEQDEMFRG..A..ADQVIVGNASLRLKN.QLTDAGTYKCYIITSKGKG.NANL.YKT
Retrocopy FVHEFKEGKDELSEQDEMFRGLIAMLADQVIVGNASLRLKNIQLTDAGTYKCYIITSKGKG<NANLAYKT

Parental  GAFSMPEVNVDYNASSETLRCEAPRWFPQPTVVWASQVDQGANFSEVSNTSFELNSENVTMKVVSVLYNV
          GAFSMPEV.VDYNASSETL.CEAP.W.P..TVV..S.VD.GA.FSEVSNT.FELNSENVTMKVVSVLY.V
Retrocopy GAFSMPEVKVDYNASSETLQCEAP*WYPRTTVV*RSLVD*GAKFSEVSNTIFELNSENVTMKVVSVLYDV

Parental  TINNTYSCMIENDIAKATGDIKVTESEIKRRSHLQLLNSKASLCVSSFLAISWALLPLAPYLMLK
          .INNTYSCMIENDI.KATGDIK.TESEIKR.SHLQLLN.K.SLC.SSF.AISWALLPLAPYLMLK
Retrocopy MINNTYSCMIENDITKATGDIKATESEIKR*SHLQLLNPKPSLCISSFFAISWALLPLAPYLMLK

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	0.08 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.12 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	18.78 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_611 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_611 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005097	1 retrocopy	retro_chof_1322,
Dasypus novemcinctus	ENSDNOG00000013317	1 retrocopy	retro_dnov_1181,
Homo sapiens	ENSG00000134258	1 retrocopy	retro_hsap_2420,
Gorilla gorilla	ENSGGOG00000025814	1 retrocopy	retro_ggor_1505,
Macaca mulatta	ENSMMUG00000016964	1 retrocopy	retro_mmul_611 ,
Nomascus leucogenys	ENSNLEG00000005256	1 retrocopy	retro_nleu_2811,
Pan troglodytes	ENSPTRG00000001164	1 retrocopy	retro_ptro_1394,