RetrogeneDB ID: retro_tsyr_2004

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_77596:6188..6944(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARDBP
• Ensembl ID: ENSTSYG00000004077
• Aliases: None
• Description: TAR DNA binding protein [Source:HGNC Symbol;Acc:11571]

Sequence

>retro_tsyr_2004
CAAATACCAGCAGAAGATGATGGGGAGGTACTACTGTTCCTGGTCACAGCCCAGTTTCCAGGGGCATGTGGGCCGTGCTA
CAGGAATTCAGTGTCTCAATGTATGAGAGATATCTGACTGGAAGAAGGAATCCTGCAAGCCCCTGATGCTGACTGGGGAA
ATTTGGTATATGTTGTTAATTAGCCCAAGGATAACAAAAGAAAAATAAATGAGATAGATACTTCATCATAAGTGAAAGTG
AAAAGAGTAGCCCAGAAAACATTCAACTTAATAATGTTGGGTCTCCTGTGGGAAACAACTGAACAGAATCTGAAACAATA
TTTTAGTACATTTGGGAAAGTGCTTATGGTGCAGGTCAAGAAAGATATTAAAACTCGTCACTCAAAAGGATTTGGCTTTG
TTCATTTTACGGAATATGAAATCCAGGTGAAAGTAATGTCATAACAACATATGAGAGATGGATGATGATGAGATTGTAAA
TTTCCTAATTCTAAGCAAAGTCCAGATGAACCCTTGAGAAGCAGAAAGGTGTTTGTGGGTGCATGTGAGGACATGACTGC
TGACAAACTGTGGCAGTTCCTCTGCTGGTACAGAGAAGAGGTGGATGTCTTTATTCGCAAGCCGTTCAGAGCCTTCACCT
TTGTCATGTTTGCAGGTGATCAGGTTGCCCAATCTCTTTCTGGAGAGGACTTGATCACTAAAGTAATCAATGTGCATATA
TCCAGTGCTGCACCTAAGCACAATAGCGATAGAAAG

Alignment

ORF - retro_tsyr_2004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.28 %
• Parental protein coverage: 61.11 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMD
          .IP.EDDG.VLL..VTAQFPGACG..YRN.VSQCMR...L.EGIL.APDA.WGNLVYVVN.PKDNKRK..
Retrocopy QIPAEDDGEVLLFLVTAQFPGACGPCYRNSVSQCMRDI*LEEGILQAPDADWGNLVYVVN*PKDNKRKIN

Parental  ETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKDYFSTFGEVLMVQVKKDIKTGHSKGFGFVRFTEYE
          E.D.SS.VKVKR..QKT..LI.LGL.W.TTEQ.LK.YFSTFG.VLMVQVKKDIKT.HSKGFGFV.FTEYE
Retrocopy EIDTSS*VKVKRVAQKTFNLIMLGLLWETTEQNLKQYFSTFGKVLMVQVKKDIKTRHSKGFGFVHFTEYE

Parental  TQVKVMSQRHMIDGRWCDCKLPNSKQSPDEPLRSRKVFVGRCTEDMTADELQQFFCQYGEVVDVFIPKPF
          .QVKVMS..HM.DG...DCK.PNSKQSPDEPLRSRKVFVG.C.EDMTAD.L.QF.C.Y.E.VDVFI.KPF
Retrocopy IQVKVMS*QHMRDG***DCKFPNSKQSPDEPLRSRKVFVGAC-EDMTADKLWQFLCWYREEVDVFIRKPF

Parental  RAFAFVTFADDQVAQSLCGEDLIIKGISVHISNAEPKHNSSRQ
          RAF.FV.FA.DQVAQSL.GEDLI.K.I.VHIS.A.PKHNS.R.
Retrocopy RAFTFVMFAGDQVAQSLSGEDLITKVINVHISSAAPKHNSDRK

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_2004 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Tarsius syrichta	ENSTSYG00000004077	1 retrocopy	retro_tsyr_2004 ,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17,