RetrogeneDB ID: retro_tsyr_1749

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_56773:3593..4500(-)
• 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_1749
CAGACCTGTCTGGGCTGTAAGAAGAATTTCTGTATGATCTCTTCAAGCCTTGTGGAGAACAGGCCCGGCTCTGCCTTCTC
TGCCAACGGTTCCAAGCCACAGGCTTTCAGCAGGAGGAGTTCATGAGGATGAATGTGAAAGACCTGAGGGACTATCTCAG
CCTCCATGACATCATCACCGAAATGTGCCAGGAGAAAGAGGAGCTGGTGCTCTTGGTGTTTGGGCAGCAACCTGTAATCT
CCCAGGAGAGCAGGACTCGTGTCCCCACCTTGTCCCTGGACTTTCTTGGACATCAAGCCTTCCTGACACAGCCTCATGCC
AGCACAGTTCCACCTACCTCACCCAATCTCCCCTCTTCGTCTCCACAAGCCACCTCTGTCACCCCAGGCCTGGCTCAGGA
AAGTCAGCAGGCGAATGGTCATGTGTCTCAGGACCAAGAGGACCCCATCTACCTGGAGAGCACAGCCAGAGTACCTGCTG
AGGATGAGACCCATTCCACTGACTCAGAACACAACTCGTCCTGGGTGGGAGGACCTCTCTGTCTGACCTGACCGACCTGC
AGGACATTGAAAGCCTGATAGTGCAGCAACTGAAGGAGATCCTGGCTTGCAACTTCATCAACTATAAGGGCTGCTGTGAG
AAGTGGGAACTGATGGAGAGTGTCACGCGGTTGTACAAGGATCAGAAAGGACTCTAGCATCTGGTGTGTGGTGCTGAAGA
CCAAAACGAAGGAGCACTGCCATCTGGCCTGGAGGAGAACCTGTGTCAAATCTGTATGAACTCACCTACTGACTGCATTC
TGCTAGAGTGTGGCCACATGGTTACCTGTACCAAGTGTGGCAAGCACATGAATGAGTGTCCTATCTGCCAGCAGTATGTG
ATCTGAGTTGTGCATGTCTTCCGGTCC

Alignment

ORF - retro_tsyr_1749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.87 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTCLDCKKHFCMTCSSQVGNGP-RLCLLCQRFRATAFQQEEFMRMNVKDLRDYLSLHDIITEMCQEKEEL
          QTCL.CKK.FCM..SS.V.N.P.RLCLLCQRF.AT.FQQEEFMRMNVKDLRDYLSLHDIITEMCQEKEEL
Retrocopy QTCLGCKKNFCMISSSLVENRP<RLCLLCQRFQATGFQQEEFMRMNVKDLRDYLSLHDIITEMCQEKEEL

Parental  VLLVFGQQPVISQESRTRVPTLSLDFLGHQAFLTQPHASTVPPTSPNLPSSSPQATSVTPGLAQESQQAN
          VLLVFGQQPVISQESRTRVPTLSLDFLGHQAFLTQPHASTVPPTSPNLPSSSPQATSVTPGLAQESQQAN
Retrocopy VLLVFGQQPVISQESRTRVPTLSLDFLGHQAFLTQPHASTVPPTSPNLPSSSPQATSVTPGLAQESQQAN

Parental  GHVSQDQEDPIYLESTARAPAEDETQSIDSEDS-FVPGRRASLSDLTDLEDIEGLTVRQLKEILARNFVN
          GHVSQDQEDPIYLESTAR.PAEDET.S.DSE....V.G.R.SLSDLTDL.DIE.L.V.QLKEILA.NF.N
Retrocopy GHVSQDQEDPIYLESTARVPAEDETHSTDSEHN<LVLGGRTSLSDLTDLQDIESLIVQQLKEILACNFIN

Parental  YKGCCEKWELMERVTRLYKDQKGLQHLVCGAEDQNGGALPSGLEENLCKICMDSPIDCVLLECGHMVTCT
          YKGCCEKWELME.VTRLYKDQKGL.HLVCGAEDQN.GALPSGLEENLC.ICM.SP.DC.LLECGHMVTCT
Retrocopy YKGCCEKWELMESVTRLYKDQKGL*HLVCGAEDQNEGALPSGLEENLCQICMNSPTDCILLECGHMVTCT

Parental  KCGKRMNECPICRQYVIRAVHVFRS
          KCGK.MNECPIC.QYVI..VHVFRS
Retrocopy KCGKHMNECPICQQYVI*VVHVFRS

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_1749 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,