RetrogeneDB ID: retro_ptro_1394

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:25259486..25260308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTCN1
• Ensembl ID: ENSPTRG00000001164
• Aliases: None
• Description: V-set domain containing T cell activation inhibitor 1 [Source:HGNC Symbol;Acc:28873]

Sequence

>retro_ptro_1394
TTCTACAGCATAATTAGCATCATCGTTACTCTGGCTGGAGCAATTGCACTCATCATTGGCTTTGGTATTTCAGGGAGACA
CTCCATCACAGTTGCTACTCTCACCTCAGCTGGGAACATTGGGGAGGATGGAATCCTGAGCTGCACTTTTGAACTTGACA
TCAAACTTTCTGATTATCATGATACAGTGGCTGAAGGAAGGGGTTATAGGCTTGGTCCATGAGTTCAAAGAAGGCAAAGA
TGAGCTGTCAGAGCAGGATGAAATGTTCAGAGGCCTGACAGCAGTGCTTGCTGATCAAGTGATAGTTGGCAATGCCTCTC
TGCAGCTGAAAAACATACAACTCACAGATGCTGGCACCTACAAATGTTATATCATCACTTCTAAAGGCAAGGGGAATGCT
AACCTTGAGTATAAAACTGGAGCCTTCAGCATGCCAGAGGTGAAAGTAGACTATAATGCCAGCTCAGAGACCTTGCGATG
TGAGGCTCCCTTATTGGTCTCTCAGCCCACAGTGGTCTGAAGATCCCTAGTTGACCAGGGAGCCAAATTCTCAGAAGTCT
CCAATACCACCTTTGAGCTGAACTCTGAGGATGTGGCCATGAAGGTTGTGTCTGTGCTCTACAATGTTACGATCAACAAC
ACATACTCCTGTATGATTGAAAATGACATTGCCAAAGCAACAGGGGATATCAAAGGACAGAATCTGAGATCAAAAGGCGG
AGTCACCTACAGCTGCTGAACTCAAAGTCTTCTCTGTGTGTCTCTTCTTTTTTTGCCATCAGCTGGACACTTCTGCTTCT
TGCCCCTTACCTGATGCTAAAA

Alignment

ORF - retro_ptro_1394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 97.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FWSIISIIIILAGAIALIIGFGISGRHSITVTTVASAGNIGEDGILSCTFEPDIKLSD-IVIQWLKEGVL
          F.SIISII..LAGAIALIIGFGISGRHSITV.T..SAGNIGEDGILSCTFE.DIKLSD.I.IQWLKEGV.
Retrocopy FYSIISIIVTLAGAIALIIGFGISGRHSITVATLTSAGNIGEDGILSCTFELDIKLSD>IMIQWLKEGVI

Parental  GLVHEFKEGKDELSEQDEMFRGRTAVFADQVIVGNASLRLKNVQLTDAGTYKCYIITSKGKGNANLEYKT
          GLVHEFKEGKDELSEQDEMFRG.TAV.ADQVIVGNASL.LKN.QLTDAGTYKCYIITSKGKGNANLEYKT
Retrocopy GLVHEFKEGKDELSEQDEMFRGLTAVLADQVIVGNASLQLKNIQLTDAGTYKCYIITSKGKGNANLEYKT

Parental  GAFSMPEVNVDYNASSETLRCEAPRWFPQPTVVWASQIDQGANFSEVSNTSFELNSENVTMKVVSVLYNA
          GAFSMPEV.VDYNASSETLRCEAP....QPTVV..S..DQGA.FSEVSNT.FELNSE.V.MKVVSVLYN.
Retrocopy GAFSMPEVKVDYNASSETLRCEAPLLVSQPTVV*RSLVDQGAKFSEVSNTTFELNSEDVAMKVVSVLYNV

Parental  TINNTYSCMIENDIAKATGDIK-VTESEIKRRSHLQLLNSKASLCVSSFFAISWALLPLSPYLMLK
          TINNTYSCMIENDIAKATGDIK..TESEIKRRSHLQLLNSK.SLCVSSFFAISW.LL.L.PYLMLK
Retrocopy TINNTYSCMIENDIAKATGDIK<RTESEIKRRSHLQLLNSKSSLCVSSFFAISWTLLLLAPYLMLK

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	0.20 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.32 RPM
SRP007412_kidney	0.00 RPM	4.97 RPM
SRP007412_liver	0.00 RPM	0.33 RPM
SRP007412_testis	0.00 RPM	2.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1394 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1394 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2420
Gorilla gorilla	retro_ggor_1505

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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 ,