RetrogeneDB ID: retro_tsyr_2011

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_79078:337..959(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000010339
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ENO1
• Ensembl ID: ENSTSYG00000002509
• Aliases: None
• Description: enolase 1, (alpha) [Source:HGNC Symbol;Acc:3350]

Sequence

>retro_tsyr_2011
ATGTCTGTTCTCAAGGTCCAGGCCAGAGAGATCTTTGACTTTTGTGGGAACTCCACTGTTGAAGTTGATCTCTATACCAC
AAAAGGTTTCTTCAGAGCTACTGTGCCCAGTGGCGCCTCAACTGGTATCAATGAGGCCCTAGAGCTCTGGCACAGTGATA
AGACATGCTATATGGGGAAGAGTGTCTCAAAGGCTGTTGAGCACATCAATAAAACTATTGAGCATGCTCTGGTTAGCAAG
AAACTGAACGTCATGAAGCAGGAGAAGATCAACAAACTGATTATTGAGATGGGATGGGATGGAACATAAATCTAAGTTTG
GTGCAAACGCCATTCTTGGGGTGTCTCTTGCTGTCTGCAAAGCTGGTGCTGTTGAAAAGGGCACTCCCCTGTACCACCAC
ATCACCAACTTGGCTGGCAACTCTGAGGTCATCCTGCCAGTCCTGACCTTCAATGTCATCAACGGTGGTTCTCATGCCGG
CAGCAAGCTGGCCATGCAGGAGTTCATGATCCTCCCCATCGGGGAAGCAAACTTCAGGGAAGTCATGCGCATTGGCACAG
AGGTTTAATACAACCTGAAGAAAGTTGTCAAGGAGAAATAATGGAATGATGCCACCAATGTG

Alignment

ORF - retro_tsyr_2011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 93.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVLKIHAREIFDSRGNPTVEVDLYTAKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSKAVEHIN
          MSVLK..AREIFD..GN.TVEVDLYT.KG.FRA.VPSGASTGI.EALEL...DKT.YMGK.VSKAVEHIN
Retrocopy MSVLKVQAREIFDFCGNSTVEVDLYTTKGFFRATVPSGASTGINEALELWHSDKTCYMGKSVSKAVEHIN

Parental  KTIAPALVSKKLNVVEQEKIDKLMIEM-DGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAG
          KTI..ALVSKKLNV..QEKI.KL.IEM.DG.E.KSKFGANAILGVSLAVCKAGAVEKG.PLY.HI..LAG
Retrocopy KTIEHALVSKKLNVMKQEKINKLIIEM>DGMEHKSKFGANAILGVSLAVCKAGAVEKGTPLYHHITNLAG

Parental  NSEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGAASFKEAMRIGAEVYHNLKNVIKEKYGKDATNV
          NSEVILPV..FNVINGGSHAG.KLAMQEFMILP.G.A.F.E.MRIG.EV..NLK.V.KEK...DATNV
Retrocopy NSEVILPVLTFNVINGGSHAGSKLAMQEFMILPIGEANFREVMRIGTEV*YNLKKVVKEK*WNDATNV

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_2011 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 12 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003483	2 retrocopies	retro_chof_1289, retro_chof_1811,
Callithrix jacchus	ENSCJAG00000000359	4 retrocopies	retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus	ENSEEUG00000008602	2 retrocopies	retro_eeur_23, retro_eeur_243,
Macropus eugenii	ENSMEUG00000005942	11 retrocopies	retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii	ENSMEUG00000007840	1 retrocopy	retro_meug_96,
Monodelphis domestica	ENSMODG00000009521	1 retrocopy	retro_mdom_1794,
Mus musculus	ENSMUSG00000063524	1 retrocopy	retro_mmus_109,
Otolemur garnettii	ENSOGAG00000004001	1 retrocopy	retro_ogar_1059,
Rattus norvegicus	ENSRNOG00000017895	1 retrocopy	retro_rnor_112,
Sarcophilus harrisii	ENSSHAG00000005522	1 retrocopy	retro_shar_304,
Tarsius syrichta	ENSTSYG00000002509	1 retrocopy	retro_tsyr_2011 ,
Tarsius syrichta	ENSTSYG00000007066	7 retrocopies	retro_tsyr_1019, retro_tsyr_1157, retro_tsyr_1626, retro_tsyr_1917, retro_tsyr_2043, retro_tsyr_52, retro_tsyr_534,