RetrogeneDB ID: retro_tsyr_1903

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_64982:9302..10146(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TM9SF3
• Ensembl ID: ENSTSYG00000000322
• Aliases: None
• Description: transmembrane 9 superfamily member 3 [Source:HGNC Symbol;Acc:21529]

Sequence

>retro_tsyr_1903
CACAAAAAACTGAAATAAGGTTTTTAATGGAAATCGAATTGTTGATGTTAATCTAACTAGTGAAGGAAAGGTGAAACTGG
TTCTGAATACTAAAATCCAGATGTCCTATTCAGTAAAATGGAAAAAGTCAGATGTAAAATTTGAAGATCGATTTGACAAA
TATCTTGATCTATCCTTTTTCCAACATAGGATTCATTGGTTTTCAATTTTCAACTCCTTCATGATGGTGGTCTTCTTGAC
GAGCTTAGTTTCAATAATTTTAATGAGAACCTTAAGAAAAGATTATGCCTGGTACAGTAAAGAAGAAATGGATGGCATGG
ACAGAGACCTAGGAGATGAGTATAGGTGGAAGCAGGTGCATGGAGATGTGTTCAGACCATCAAGTCACCCTCTAATATTC
TCCTCCCTCATTGGCTCTGGCTGCCAGATATTTGCGGTGTCTCTCATTGCCATTATTGTTGCAATGATAGAAGATCTGTA
TACAGAGAGGGGATCGATGCTCAGTATGGCCATATATGTCTATGCTGCTATGTCTCCAGTGAATGGTTATTTTGGAAGAA
GTCTGTATGCTAGACAAGGAGGAAGAAGATGGATGAAACAGATGTTTATTGGGACATTCCTCATCCCAGCTATGGTGTGT
GGCACTGCCTTCTTCATCAATTTCATAGCCATTTACTACCATGCTTCAAGAGCCATTCCTTTCGGAACAATGGTAGCTGT
TTGTTGCATCTGTTTTTTTGTTATTCTTCCTCCAAATCTTGTTGGTACAATACTTGGCCGAAATCCATCAGGTCAGTCCA
ACTTTCCTTGTCATGTCCATACTGTGCCTCATCCTATACCAGAG

Alignment

ORF - retro_tsyr_1903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 50.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YKKLEIGF-NGNRIVDVNLTSEGKVKLVPNTKIQMSYSVKWKKSDVKFEDRFDKYLDPSFFQHRIHWFSI
          .KKL..GF.NGNRIVDVNLTSEGKVKLV.NTKIQMSYSVKWKKSDVKFEDRFDKYLD.SFFQHRIHWFSI
Retrocopy HKKLK*GF>NGNRIVDVNLTSEGKVKLVLNTKIQMSYSVKWKKSDVKFEDRFDKYLDLSFFQHRIHWFSI

Parental  FNSFMMVIFLVGLVSMILMRTLRKDYARYSKEEEMDDMDRDLGDEYGWKQVHGDVFRPSSHPLIFSSLIG
          FNSFMMV.FL..LVS.ILMRTLRKDYA.YSKEE.MD.MDRDLGDEY.WKQVHGDVFRPSSHPLIFSSLIG
Retrocopy FNSFMMVVFLTSLVSIILMRTLRKDYAWYSKEE-MDGMDRDLGDEYRWKQVHGDVFRPSSHPLIFSSLIG

Parental  SGCQIFAVSLIVIIVAMIEDLYTERGSMLSTAIFVYAATSPVNGYFGGSLYARQGGRRWIKQMFIGAFLI
          SGCQIFAVSLI.IIVAMIEDLYTERGSMLS.AI.VYAA.SPVNGYFG.SLYARQGGRRW.KQMFIG.FLI
Retrocopy SGCQIFAVSLIAIIVAMIEDLYTERGSMLSMAIYVYAAMSPVNGYFGRSLYARQGGRRWMKQMFIGTFLI

Parental  PAMVCGTAFFINFIAIYYHASRAIPFGTMVAVCCICFFVILPLNLVGTILGRNLSGQPNFPCRVNAVPRP
          PAMVCGTAFFINFIAIYYHASRAIPFGTMVAVCCICFFVILP.NLVGTILGRN.SGQ.NFPC.V..VP.P
Retrocopy PAMVCGTAFFINFIAIYYHASRAIPFGTMVAVCCICFFVILPPNLVGTILGRNPSGQSNFPCHVHTVPHP

Parental  IPE
          IPE
Retrocopy IPE

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_1903 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000013527	1 retrocopy	retro_nleu_387,
Tarsius syrichta	ENSTSYG00000000322	2 retrocopies	retro_tsyr_1760, retro_tsyr_1903 ,