RetrogeneDB ID: retro_tsyr_1107

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_30771:386..1068(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF1D
• Ensembl ID: ENSTSYG00000014258
• Aliases: None
• Description: TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa [Source:HGNC Symbol;Acc:28759]

Sequence

>retro_tsyr_1107
GTTCCTTACTCACCTAAATGGGGGCAAAGAAGCCCAATTAGGAAATTTGTTCATTCACCTGAAAATGTTCAAGCAAGAGA
TTCATCGTCAAGTGACTCATCTTTTGAACCAAGACCACTGACTTTAAAAGCTATTTTTGAAAGATTCAAGAAAAAGAAGC
GTAAATAGAGGAAATGCGGAAATGGGAAGACCAAGGGGAAGACCGAAAGGAAGAAGACATAGTCGACGCTCACAAATAGA
TAAGAAACAGTGTAAAAGCAAAGGATCTGGCTTCCCTTTTGTAGAATCAGAGAATGGCAGAAAACAATTACCTTGGAGAA
AAATATTAACCTTTGAGCAAGCTGTTGCAAGAGGGTTTTTAGCTACATTGAAAAACTGAAGTACGAACACCACCTAAAAG
AATCTATGAAACAAATGGATGTTGGTTAAGATTTAGGAAAAGAAGATCTTGATAGTCGTAGATATAAATATTAGAGTGAC
GATGGATCCATTTCTCCTATTGAAGAATCAACAGCAGAGGATGAGGATGTAGCACCTCTTGAACACGATGAATGTGATAT
CAAATTGGCAGGGGATAGTTTCATATTAAGTTTTGAGTTCCCAGTGACAATGGGAACAAGAGAATACTGAAGAAGTTGCT
TTGTTTAAAAAGAGAACAGAGAACAGAGACATAGGCCAGAGG

Alignment

ORF - retro_tsyr_1107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.12 %
• Parental protein coverage: 92.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VPCSPKRRQRSPIRKFVHSPENVQARDSSSSDSSFEPRPLSLKAIFERFKKKKRTK-RKYKPTGRRRGRP
          VP.SPK..QRSPIRKFVHSPENVQARDSSSSDSSFEPRPL.LKAIFERFKK.K..K.R.....GR.RGRP
Retrocopy VPYSPKWGQRSPIRKFVHSPENVQARDSSSSDSSFEPRPLTLKAIFERFKK-KKRK>RGNAEMGRPRGRP

Parental  EGRKNSRRSQIDKKQCKSKGSGFPFVESENGRKPLPWRKILIFEQAVARGF-FNYIEKLKYEHHLKESLK
          .GR..SRRSQIDKKQCKSKGSGFPFVESENGRK.LPWRKIL.FEQAVARGF.F.YIEKLKYEHHLKES.K
Retrocopy KGRRHSRRSQIDKKQCKSKGSGFPFVESENGRKQLPWRKILTFEQAVARGF<FSYIEKLKYEHHLKESMK

Parental  QMDVGEDLEKEDLDSRRYKYLDDDGSISPIEESIAEDEDAAPLEHDECDIKLAGDSFILSSEFPVTM-QE
          QMDVG.DL.KEDLDSRRYKY..DDGSISPIEES.AEDED.APLEHDECDIKLAGDSFILS.EFPVTM...
Retrocopy QMDVG*DLGKEDLDSRRYKY*SDDGSISPIEESTAEDEDVAPLEHDECDIKLAGDSFILSFEFPVTM>EQ

Parental  NTEE-VALSKKRTE-RDIGQK
          ...E.VAL.KKRTE.RDIGQ.
Retrocopy ENTEEVALFKKRTENRDIGQR

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_1107 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013436	1 retrocopy	retro_chof_405,
Myotis lucifugus	ENSMLUG00000011431	1 retrocopy	retro_mluc_2033,
Monodelphis domestica	ENSMODG00000008546	1 retrocopy	retro_mdom_1216,
Oryctolagus cuniculus	ENSOCUG00000001096	2 retrocopies	retro_ocun_101, retro_ocun_23,
Otolemur garnettii	ENSOGAG00000002521	1 retrocopy	retro_ogar_1139,
Sarcophilus harrisii	ENSSHAG00000005874	1 retrocopy	retro_shar_566,
Tarsius syrichta	ENSTSYG00000014258	1 retrocopy	retro_tsyr_1107 ,