RetrogeneDB ID: retro_tsyr_1756

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_569820:45..645(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VIM
• Ensembl ID: ENSTSYG00000004937
• Aliases: None
• Description: vimentin [Source:HGNC Symbol;Acc:12692]

Sequence

>retro_tsyr_1756
GAGATGCTTTGGAGAGAGGAAGCCGAGAGCACCCTGCAATCTTTCAGCCAGGATGTTGACAACGCATCTCTGGCACGTCT
TGACCTTGAAGGTAAAGTGGAATCCTTGCGAGAAGAGATCGCCTTTTTGAAGAAACGACACGATGAGGCAATCCAGGAGT
TGCGGGCCCAGATCCAGGAACTGCACGTCCAGGTTGATGTGGAGGTCTCCAAGCCCGACCTCACAGCTGCCCTGCTTCAC
ATATGCCAGCAGTATGGAAGTGTGGCTGCCAAGAACCTTCAGGAGGCAGAAGAATGGTACAAGACCAAGTTTGCTGACCT
CTCTGGGGCTGCTAACTGGAACAACGATGCCCTGTGCCAGGCGAACCAGGCGTCCAATGAGTCCCGGAGATAGGCGCAGT
CCCTCACCTGTGAAGTGGATGCCCTTCAAGGAACCAACGAGTCCCTGGAATGCCAGACGTGTGAAACGGAAGAGAACTTT
GCTGTTGAAATTGCTAACTACCAAGACACTATCGGCCGCCTGAAGCGTGAGATTCAGAACACGAAAGAATAAATGGCTCC
TCACCTTCTTGAATACCAAGACCTACTCAGTGTCAAGATG

Alignment

ORF - retro_tsyr_1756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 71.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EMLQREEAESTLQSFRQDVDNASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQEQHVQIDVDVS
          EML.REEAESTLQSF.QDVDNASLARLDLE.KVESL.EEIAFLKK.HDE.IQEL.AQIQE.HVQ.DV.VS
Retrocopy EMLWREEAESTLQSFSQDVDNASLARLDLEGKVESLREEIAFLKKRHDEAIQELRAQIQELHVQVDVEVS

Parental  KPDLTAALRDVRQQYESVAAKNLQEAEEWYKSKFADLSEAANRNNDALRQAKQESNEYRRQVQSLTCEVD
          KPDLTAAL....QQY.SVAAKNLQEAEEWYK.KFADLS.AAN.NNDAL.QA.Q.SNE.RR..QSLTCEVD
Retrocopy KPDLTAALLHICQQYGSVAAKNLQEAEEWYKTKFADLSGAANWNNDALCQANQASNESRR*AQSLTCEVD

Parental  ALKGTNESLERQMREMEENFAVEAANYQDTIGRLQDEIQNMKEEMARHLREYQDLLNVKM
          AL.GTNESLE.Q..E.EENFAVE.ANYQDTIGRL..EIQN.KE.MA.HL.EYQDLL.VKM
Retrocopy ALQGTNESLECQTCETEENFAVEIANYQDTIGRLKREIQNTKE*MAPHLLEYQDLLSVKM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1756 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008688	2 retrocopies	retro_cjac_1026, retro_cjac_1456,
Dasypus novemcinctus	ENSDNOG00000011305	1 retrocopy	retro_dnov_72,
Tarsius syrichta	ENSTSYG00000004937	2 retrocopies	retro_tsyr_1756 , retro_tsyr_564,