RetrogeneDB ID: retro_tsyr_1455

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_447476:263..1055(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000011189
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSTSYG00000013641
• Aliases: None
• Description: 3-oxoacid CoA transferase 1 [Source:HGNC Symbol;Acc:8527]

Sequence

>retro_tsyr_1455
AAAGACTGGAGTAAAATGACTAACAGTGGAGGGGTTGACAACTTTGACTTGGACTTTATGCGGTGATCCAAGCAGATAAA
ATGCATGGTCTCTTTATATGTGGGAGAAAATACAAAATTTGAATGACAGCTCTATCTGGTGAATTAGAAGCAGAGCTAAC
ACCTCAGGACACACTTGCAGAAAGGATTCATGCAGGTAGGGCTGGGGTTTCTGCATTTTACACCACCACAGGAGATGGGA
CCCTGGTACAAGAAGAAGGATCGTCCACCAAATACAATAAGGATGGCAGCATTGTCACTGCCAGCAAGCCAAGAGAGGTG
AGGGAATTCAGTGGTTAACACTTTATTTTGGAGAAAGCAATTACGGGGCATTTTGCTTTGGTGAAAGCATGGAAGGCAAA
CCCAGAAGGAAACATGATTTTCAGAAAAAGTGCAAGGAATTTCAACTTGCTCATGCACGCAATTGCAGAAACCATAGGGG
TAGAGGTTGAAGAAATTGTGGCTATTGGATTATTTGCTCCAAAGACGTCCATATTCCCAAGATTTATGTACATCACCTTA
TAAAGGGAGAAAAATATGAGAAAAGAAGTGAGCACTTAACAATCCAGAAAGAGAGAGACGGAAATGTTAGATCTGGTAAC
ATGGAGATAATGCAAGAAAATGTATCATCAAGCAGGCAGCTCCTGAACTTGAGGACGGCACATATGCTAACTTGGGCATA
GGAATCAATCCTCTGGCCAGCAACCTTATCAGCCCAAATATGAGCGTTCGTGTGTAGAATGGAAATGGAGTC

Alignment

ORF - retro_tsyr_1455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.28 %
• Parental protein coverage: 51.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KGLTAISNNAGVDNFGLGLLLRSKQIKRMVSSYVGENAEFERQY-LAGELEVELTPQGTLAERIRAGGAG
          K......N..GVDNF.L.....SKQIK.MVS.YVGEN..FE.Q..L.GELE.ELTPQ.TLAERI.AG.AG
Retrocopy KDWSKMTNSGGVDNFDLDFMR*SKQIKCMVSLYVGENTKFE*QL<LSGELEAELTPQDTLAERIHAGRAG

Parental  VPAFYTSTGYGTLVQEGGAPIKYNKDGSIAIASKPREVREFNGQHFILEEAITGDFALVKAWKADRAGNV
          V.AFYT.TG.GTLVQE.G...KYNKDGSI..ASKPREVREF.G.HFILE.AITG.FALVKAWKA...GN.
Retrocopy VSAFYTTTGDGTLVQEEGSSTKYNKDGSIVTASKPREVREFSG*HFILEKAITGHFALVKAWKANPEGNM

Parental  TFRKSARNFNLPMCKAAETTVVEVEEIVDIGSFAP-EDIHIPQIYVHRLIKGEKYEKRIERLSIRKEGDG
          .FRKSARNFNL.M...AET..VEVEEIV.IG.FAP..D.HIP.IYVH.LIKGEKYEKR.E.L.I.KE.DG
Retrocopy IFRKSARNFNLLMHAIAETIGVEVEEIVAIGLFAP<KDVHIPKIYVHHLIKGEKYEKRSEHLTIQKERDG

Parental  KAKSTK-PGDNVRERIIKRAALEFEDGMYANLGIGIPLLASNFISPNMTVHLQSENGV
          ...S....GDN.R..IIK.AA.E.EDG.YANLGIGI..LASN.ISPNM.V.....NGV
Retrocopy NVRSGN<HGDNARKCIIKQAAPELEDGTYANLGIGINPLASNLISPNMSVRV*NGNGV

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_1455 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033186	2 retrocopies	retro_btau_1243, retro_btau_1302,
Dipodomys ordii	ENSDORG00000016318	1 retrocopy	retro_dord_282,
Equus caballus	ENSECAG00000018312	1 retrocopy	retro_ecab_511,
Homo sapiens	ENSG00000083720	1 retrocopy	retro_hsap_14,
Gorilla gorilla	ENSGGOG00000025087	1 retrocopy	retro_ggor_378,
Myotis lucifugus	ENSMLUG00000009431	1 retrocopy	retro_mluc_194,
Nomascus leucogenys	ENSNLEG00000016656	1 retrocopy	retro_nleu_2438,
Oryctolagus cuniculus	ENSOCUG00000009231	1 retrocopy	retro_ocun_672,
Otolemur garnettii	ENSOGAG00000009909	2 retrocopies	retro_ogar_2773, retro_ogar_2781,
Pongo abelii	ENSPPYG00000015428	2 retrocopies	retro_pabe_336, retro_pabe_478,
Pan troglodytes	ENSPTRG00000016829	1 retrocopy	retro_ptro_140,
Rattus norvegicus	ENSRNOG00000043094	2 retrocopies	retro_rnor_2177, retro_rnor_2256,
Ictidomys tridecemlineatus	ENSSTOG00000008271	1 retrocopy	retro_itri_747,
Tarsius syrichta	ENSTSYG00000013641	1 retrocopy	retro_tsyr_1455 ,
Tursiops truncatus	ENSTTRG00000004331	1 retrocopy	retro_ttru_875,
Vicugna pacos	ENSVPAG00000002550	1 retrocopy	retro_vpac_556,