RetrogeneDB ID: retro_tsyr_846

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_215910:2981..3774(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBAP1
• Ensembl ID: ENSTSYG00000013035
• Aliases: None
• Description: ubiquitin associated protein 1 [Source:HGNC Symbol;Acc:12461]

Sequence

>retro_tsyr_846
GAGAAACATTCTGGTAGAAAAATTCTGTTAGGAGCCACTGCACCAATTATGACTCAGTTATTGGACAGTAACTTACCAAG
AGGAGGCTCTGGGTTTGTGTTACAAGATGAAGTGGTCCTGGCATCCTTGGAGTGGGTAACCTTAAATTTCAAATCTCTTC
ATAAACTCAAAGGCTTTATAACCTTATCACAGTTGGGTAACTATGAAAAGATGTCACTGTCTTCCAAAGTGTCCTTCTCC
CCATCCCTGCAGTAAGCAATATCAAATCCCTGTCCTTCCCCTAACCTGACTCTGATGACAGCAATCACAAGACAGCCAAG
CTGGCAAGCACTTTCCATAGCACATTCTGCCTCCACAATGGCACGTTCCAGAATTCCCTAAAGCCTTTCACCCAAAGCAG
TGCCAGAGAGCTCAATGGACATCATACTCTGGGACTTTCAGCTTTGAACTTGAACAGTAGCACAGAGATGCCAGTGCTAA
AACCTTCCCAGATGCCTTCCCTCTGGGTTTTGTCTGTGTGCACAAAGAATCATCTCCAAATATAGGTCCTATGGTCACCT
CTCCCAATTTCTCAATGTCACAAGTGCCCAACATGCCCGGCTTTCTCCATGCCTATTCTGAATTGTAGATGCTGTCCCCC
AGTGAGTGGCAGTGTGTGGAGACAGTAGTCATCAAGGGCTACTCATATGAGTGTGTTGTGACAGCCATGTAGAAAAAAGG
GGAAAATATTAAGCAAATTCTCAACTATCTATTTGCACATGGACAGCTTGGTAAGAGGGGCTTCTACCCTCTT

Alignment

ORF - retro_tsyr_846 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.28 %
• Parental protein coverage: 65.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKEELRNILVGTTGPIMAQLLDSNLPRGGSGSVLQDEEVLASLERATLDFKPLHKPNGFITLPQLGNCEK
          EK...R.IL.G.T.PIM.QLLDSNLPRGGSG.VLQDE.VLASLE..TL.FK.LHK..GFITL.QLGN.EK
Retrocopy EKHSGRKILLGATAPIMTQLLDSNLPRGGSGFVLQDEVVLASLEWVTLNFKSLHKLKGFITLSQLGNYEK

Parental  MSLSSKVS-LPPIPAVSNIKSLSFPKLDSDDSNQKTAKLASTFHSTSCLRNGTFQNSLKPFTQSSASDLN
          MSLSSKVS.L.PIPAVSNIKSLSFP..DSDDSN.KTAKLASTFHST.CL.NGTFQNSLKPFTQSSA..LN
Retrocopy MSLSSKVS<LLPIPAVSNIKSLSFP*PDSDDSNHKTAKLASTFHSTFCLHNGTFQNSLKPFTQSSARELN

Parental  AHCTLGLSALNLDNGTEMPTLASSLMPSLSVLSVCT-EESLPNVTP----PNFAMSQVPNMPSCPQAYPE
          .H.TLGLSALNL...TEMP.L..S.MPSL.VLSVCT..ES.PN..P....PNF.MSQVPNMP....AY.E
Retrocopy GHHTLGLSALNLNSSTEMPVLKPSQMPSLWVLSVCT<KESSPNIGPMVTSPNFSMSQVPNMPGFLHAYSE

Parental  LQTLSPSERQCVETVVNMGYSYECVLRAMKKKGENIEQILDYLFAHGQLCEKGFDPL
          L..LSPSE.QCVETVV..GYSYECV..AM.KKGENI.QIL.YLFAHGQL...GF.PL
Retrocopy L*MLSPSEWQCVETVVIKGYSYECVVTAM*KKGENIKQILNYLFAHGQLGKRGFYPL

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_846 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011672	1 retrocopy	retro_eeur_466,
Myotis lucifugus	ENSMLUG00000013063	1 retrocopy	retro_mluc_2305,
Otolemur garnettii	ENSOGAG00000015802	1 retrocopy	retro_ogar_557,
Ochotona princeps	ENSOPRG00000009100	3 retrocopies	retro_opri_355, retro_opri_477, retro_opri_680,
Ictidomys tridecemlineatus	ENSSTOG00000028294	1 retrocopy	retro_itri_1318,
Tarsius syrichta	ENSTSYG00000013035	2 retrocopies	retro_tsyr_1908, retro_tsyr_846 ,