RetrogeneDB ID: retro_tsyr_738

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_186004:1079..1587(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD1
• Ensembl ID: ENSTSYG00000002894
• Aliases: None
• Description: RAD1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9806]

Sequence

>retro_tsyr_738
ATGTGTTACCAAGGTTATGGCTATCCTTAGCTGCTATTTCTGGAAGAAGGAGGAGTGGTGACAGTCTGCAAATCAATACT
CAAGAGCCTGAAGAGACACTGGATTTTGATTTCTGTGGCACCGATGTTATTAATAAAATTATTCTGCAGTCAGAGGGGCT
CTGTGAAACATTTTCCAAACTGGATATGATGAATGAGGTCCTATAGATTGTCATGTCTCCTGACAAACTTATTTCAGGTT
TTCTACTTTGGGAAATACAGGAGGCTCCCATCTTGAATATGCCACAGATTCTGATGTGATGGAAGCACTTCACTGTAATC
AGACCCAGGTCAACAGATACAAGATTTCTTTACAACCCTTTATGAAGGCATTAGTCCTATCTTGTAAGTTGTCTGTCCAA
ACAGATCACCAAGGATTCCTCTCATTACAGCATATGATTAGACGTGACGATAGACACATATGTTTTGTGGAATATTACTG
CTGCCATGATGGACATGTTCTGAAATCT

Alignment

ORF - retro_tsyr_738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.99 %
• Parental protein coverage: 60.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCYQGYGYPLMLFLEEGGVVTVCK-INTQEPEETLDFDFCSTNVINKIILQSEGLREAFSELDMTSDVLQ
          MCYQGYGYP..LFLEEGGVVTVCK.INTQEPEETLDFDFC.T.VINKIILQSEGL.E.FS.LDM...VL.
Retrocopy MCYQGYGYP*LLFLEEGGVVTVCK<INTQEPEETLDFDFCGTDVINKIILQSEGLCETFSKLDMMNEVL*

Parental  ITMSPDK-PYFRLSTFGNAGSSHLDYPKDSDLVEAFHCNQTQVNRYKISLLKPSTKALVLSCKVSIRIDN
          I.MSPDK..YFR.ST.GN.G.SHL.Y..DSD..EA.HCNQTQVNRYKIS.L.P..KALVLSCK.S...D.
Retrocopy IVMSPDK<TYFRFSTLGNTGGSHLEYATDSDVMEALHCNQTQVNRYKIS-LQPFMKALVLSCKLSVQTDH

Parental  RGFLSLQYMIRNEDGQICFVEYYCCPDEEVSES
          .GFLSLQ.MIR..D..ICFVEYYCC.D..V..S
Retrocopy QGFLSLQHMIRRDDRHICFVEYYCCHDGHVLKS

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_738 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018514	1 retrocopy	retro_cjac_1004,
Homo sapiens	ENSG00000113456	1 retrocopy	retro_hsap_634,
Gorilla gorilla	ENSGGOG00000004219	1 retrocopy	retro_ggor_555,
Macaca mulatta	ENSMMUG00000030184	1 retrocopy	retro_mmul_54,
Nomascus leucogenys	ENSNLEG00000014437	1 retrocopy	retro_nleu_455,
Otolemur garnettii	ENSOGAG00000014822	2 retrocopies	retro_ogar_2296, retro_ogar_2726,
Pongo abelii	ENSPPYG00000015389	1 retrocopy	retro_pabe_564,
Pan troglodytes	ENSPTRG00000016783	1 retrocopy	retro_ptro_462,
Tarsius syrichta	ENSTSYG00000002894	1 retrocopy	retro_tsyr_738 ,