RetrogeneDB ID: retro_tsyr_2060

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_84544:567..1467(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFFL
• Ensembl ID: ENSTSYG00000008923
• Aliases: None
• Description: ring finger and FYVE-like domain containing E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:24821]

Sequence

>retro_tsyr_2060
CAGACCTGCCTGGACTGTAAGAAGAATTTCTGCATGACCCTTCAGAGCCAAGTCTGGAATGGGTCCTGCCTCTGCCTTCT
CTGCCAATGGTTCTGAGTCACAGCCTTTCAGTGGGAGGAGCTCATGAAGATGAAGGTGAAGAACCTGAGGCACTATCTCA
GTCTCCATTATGTCTCCACCGAAATGTGCCAGGAGGAAGAGGAACTGGAGCTCTTGGTGCTTGGCCAGCAGCCTATAACT
TCCCAGAAGGGCAGGATTTATGCCCCCACCTTGTCCCTGGACTTCCCTGAGCATCAGACCTTCCTAACTCAGCCTCACTG
CAGCACAGTTCCGCCTACCTCACCTAACCTCCCATCTTCATCTCCACAAGTCCCCTCTATTGCCCCAGCCGGGGCTCAGA
AAAGTCAGCAGGCCAAAGGCCATGTGTCTCAGGACCAAGGTGACTCCATTTACCTGGGGAGCACAGCCAGAATACCTGCT
GGGGATGAGACCCAGTCCATTGACTCAGAAGACAGCATCATCCCAGGCCAGAGGACCACTCTATCTGACCCGACTGACCT
GGTGGACATTAACAATGCGGCAGCTGAAGGAGATGCTGGCTTGCAACTTTGTCAACTACAAGGGCTGCTGTGAGAAGTGG
GAGCTGATGGAGAGGGTCATGCTGTTGTACAAGCATCAGAAAGGACTTCAGCGTCTGACGTGTGGTACTGAAAACCAAAA
CAGAGGAGCCCTGCCATCTGGCCTGAAGGAGATCCTGTGTAAAATCTTCATGGACTCACCTATTGACTATGTTCTGCTGG
AGTGTGGCCACATGGTTACCTGTACCAACTGTGGCAAGCACATGAATGAGTGTCCTATCTGCCAGCAGTATGTGATCGAT
CTGTGCATGTATTCTGGTCC

Alignment

ORF - retro_tsyr_2060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTCLDCKKHFCMTCSSQVGNGPRLCLLCQRFRATAFQQEEFMRMNVKDLRDYLSLHDIITEMCQEKEELV
          QTCLDCKK.FCMT..SQV.NG..LCLLCQ.F..TAFQ.EE.M.M.VK.LR.YLSLH...TEMCQE.EEL.
Retrocopy QTCLDCKKNFCMTLQSQVWNGSCLCLLCQWF*VTAFQWEELMKMKVKNLRHYLSLHYVSTEMCQEEEELE

Parental  LLVFGQQPVISQESRTRVPTLSLDFLGHQAFLTQPHASTVPPTSPNLPSSSPQATSVTPGLAQESQQANG
          LLV.GQQP..SQ..R...PTLSLDF..HQ.FLTQPH.STVPPTSPNLPSSSPQ..S..P..AQ.SQQA.G
Retrocopy LLVLGQQPITSQKGRIYAPTLSLDFPEHQTFLTQPHCSTVPPTSPNLPSSSPQVPSIAPAGAQKSQQAKG

Parental  HVSQDQEDPIYLESTARAPAEDETQSIDSEDSFVPGRRASLSDLTDLEDIEG-LTVRQLKEILARNFVNY
          HVSQDQ.D.IYL.STAR.PA.DETQSIDSEDS..PG.R.....L.D..D....LT.RQLKE.LA.NFVNY
Retrocopy HVSQDQGDSIYLGSTARIPAGDETQSIDSEDSIIPGQRTT---LSDPTDLVD>LTMRQLKEMLACNFVNY

Parental  KGCCEKWELMERVTRLYKDQKGLQHLVCGAEDQNGGALPSGLEENLCKICMDSPIDCVLLECGHMVTCTK
          KGCCEKWELMERV..LYK.QKGLQ.L.CG.E.QN.GALPSGL.E.LCKI.MDSPID.VLLECGHMVTCT.
Retrocopy KGCCEKWELMERVMLLYKHQKGLQRLTCGTENQNRGALPSGLKEILCKIFMDSPIDYVLLECGHMVTCTN

Parental  CGKRMNECPICRQYVI-RAVHVFRS
          CGK.MNECPIC.QYVI.R.VHVF.S
Retrocopy CGKHMNECPICQQYVI<RSVHVFWS

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_2060 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001950	2 retrocopies	retro_chof_1069, retro_chof_285,
Macropus eugenii	ENSMEUG00000012628	1 retrocopy	retro_meug_1745,
Ochotona princeps	ENSOPRG00000011769	1 retrocopy	retro_opri_385,
Tarsius syrichta	ENSTSYG00000008923	2 retrocopies	retro_tsyr_1749, retro_tsyr_2060 ,