RetrogeneDB ID: retro_tsyr_1136

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_31874:3939..4542(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBADH
• Ensembl ID: ENSTSYG00000014191
• Aliases: None
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:HGNC Symbol;Acc:4907]

Sequence

>retro_tsyr_1136
TGTTCCAGGTCAAAGACTTCTAAGATTCTAGTTGGACACACTGGACTGGACAACATAGGGAATCCAATGGCAAAAAAATC
TCATGAAACATGGTTTCTTATATCTGCTTATTATTCATGATGTGTTTCCTGATGCATGTAAATAATGTCAAAATGTGGGT
GAACAGGTTGTATCTTCCCCAGCAGATGCAGCTGAAAAGGTGACAGAATGATGACAATGCTACCCACCAGTAAGAATGCA
ATAGAAGCTTATTCTGGAGCAAATGGCATTCTAAAAAAAGTGAAGGAAGGCTTATTATTAGTAGATGCCAGTACTATTGA
TCCTGCAATTTCAAAAGAATGGGCCAAAGAAACTGAGGAAATGAGAGCAGTTTTCACGGACACCCCTGTTTCTGGTGATG
TAGGAGCTGCTGGGTCTGGGAACCTTACGTTGATGGAAGGAGGAATTGAAGATGAATTTGCTGCTGCCCAAGGGTTGCTG
GGTGTATGGGTTCCAGTGTGGTGTATTGTTGAGACTGGGTAGGCTGCAAAGATCTGCAAAAACATGCTGTTAACTATTAG
TATGACCGGAACCACTGAAGCTATGAGTCTTGGAATCAGTTTA

Alignment

ORF - retro_tsyr_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.36 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CSRSVASKTPVGFIGLGNMGNPMAK-NLMKHG--YPLIIYDVFPDACKEFQDAGEQVVSSPADVAEKA-D
          CSRS..SK..VG..GL.N.GNPMAK.NLMKHG..Y.LII.DVFPDACK..Q..GEQVVSSPAD.AEK..D
Retrocopy CSRSKTSKILVGHTGLDNIGNPMAK>NLMKHGFLYLLIIHDVFPDACK*CQNVGEQVVSSPADAAEKV<D

Parental  RIITMLPTSMNAIEAYSGANGILKKVKKGSLLIDSSTIDPAVSKELAKEVEKMGAVFMDAPVSGGVGAAR
          R..TMLPTS.NAIEAYSGANGILKKVK.G.LL.D.STIDPA.SKE.AKE.E.M.AVF.D.PVSG.VGAA.
Retrocopy RMMTMLPTSKNAIEAYSGANGILKKVKEGLLLVDASTIDPAISKEWAKETEEMRAVFTDTPVSGDVGAAG

Parental  SGNLTFMVGGVEDEFAAAQELLGCMGSNVVYCGAVGTGQAAKICNNMLLAISMIGTAEAMNLGIRL
          SGNLT.M.GG.EDEFAAAQ...G..G..V.....V.TG.AAKIC.NMLL.ISM.GT.EAM.LGI.L
Retrocopy SGNLTLMEGGIEDEFAAAQ---GLLGVWVPVWCIVETG*AAKICKNMLLTISMTGTTEAMSLGISL

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_1136 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Mus musculus	ENSMUSG00000029776	1 retrocopy	retro_mmus_2360,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,
Ictidomys tridecemlineatus	ENSSTOG00000004108	1 retrocopy	retro_itri_395,
Tarsius syrichta	ENSTSYG00000014191	1 retrocopy	retro_tsyr_1136 ,
Vicugna pacos	ENSVPAG00000012531	1 retrocopy	retro_vpac_571,