RetrogeneDB ID: retro_tsyr_1373

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_417552:128..836(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXW2
• Ensembl ID: ENSTSYG00000008021
• Aliases: None
• Description: F-box and WD repeat domain containing 2 [Source:HGNC Symbol;Acc:13608]

Sequence

>retro_tsyr_1373
GACAACACTGTGGCCTGCTGGGAGTGGAATTCCAGAGCTAGGACCCAGCACTCTCAGGGGCACCTGGGGGTGGTGTTTAG
TGTGGACTACAATGATTATCTGGATATCTTGGTGAGTGGCTTTGCAGACTTCACTGTGAAAGTATGGGCTTTATCAGCTA
GGACATGCCTGAACACACTCACTGGGCAAATGGAATGGGTCACCAAGGTGGTTTGCAGAAGTGCAAAGTCAAGTCTCTCT
TGCACACCTCTGGAGACTGTATCCTCTTAAATGCAGACAAGTATGGGATTAAGATTTGACCAACTGGGAGAGAAATCAAC
TGCAAGTACTTAAAGACATTGTCTCTGAGGGAGGAAGTATCTGCCTATAGCCAAGACTTCATTTTGATGGAAAATACATT
GTCTGTAGTTCCACACTCTACCAGTGGGACTTTTTCAGTTATGATATTCTTAGTGTCCTCAAGACTCCTAAGATAGCAAA
CTTGACTTTGCTTGACTTGGAGATATCTTTGCCCTGCTGTTTGACAACTGCTACCTGTATATCATGGACTTGTAGACAGA
GAGCCTGATTAGTCGCTGGTCTGTGCCAGAATACAGGAAATCAAAGACAGGCTGAAGCTTCCTGGCAGGTGAAGCACCTT
GGCTGAATGAACTGGGCAGGCACAATGACACAGGCTTGGTCTTTGCCACCAGCATGACGGACCACAGT

Alignment

ORF - retro_tsyr_1373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.42 %
• Parental protein coverage: 52.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DNTVACWEWSSGARTQHFRGHTGAVFSVDYNDDLDILVSGSADFTVKVWALSAGTCLNTLTGHTEWVTKV
          DNTVACWEW.S.ARTQH..GH.G.VFSVDYND.LDILVSG.ADFTVKVWALSA.TCLNTLTG..EWVTKV
Retrocopy DNTVACWEWNSRARTQHSQGHLGVVFSVDYNDYLDILVSGFADFTVKVWALSARTCLNTLTGQMEWVTKV

Parental  V-LQKCKVKSLLHSPGDYILLSADKYEIKIWPIGREINCK-CLKTLSVSEDRSICLQPRLHFDGKYIVCS
          V.LQKCKVKSLLH..GD.ILL.ADKY.IKI.P.GREINCK..LK...VSE..SICL.PRLHFDGKYIVCS
Retrocopy V<LQKCKVKSLLHTSGDCILLNADKYGIKI*PTGREINCK<VLKDI-VSEGGSICL*PRLHFDGKYIVCS

Parental  SALGLYQWDFASYDILRVIKIPEIANLALLGF-GDIFALLFDNRYLYIMDLRTESLISRWPLPEYRKSKR
          S.L..YQWDF.SYDIL.V.K.P.IANL.LL...GDIFALLFDN.YLYIMDL.TESLISRW..PEYRKSK.
Retrocopy STL--YQWDFFSYDILSVLKTPKIANLTLLDL<GDIFALLFDNCYLYIMDL*TESLISRWSVPEYRKSKT

Parental  GSSFLAGEASWLNGLDGHNDTGLVFATSMPDHS
          G.SFLAGEA.WLN.L..HNDTGLVFATSM.DHS
Retrocopy G*SFLAGEAPWLNELGRHNDTGLVFATSMTDHS

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_1373 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000018687	1 retrocopy	retro_rnor_2358,
Tarsius syrichta	ENSTSYG00000008021	1 retrocopy	retro_tsyr_1373 ,