RetrogeneDB ID: retro_tsyr_1908

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_65340:8692..9465(+)
• 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_1908
CTATTGGACAATAACTTGTCCAGAAGAGGCTCTGGGTCTGTGTTATAGGAGGAAGAGAACCTAGCATCCTTGGAGTGGGC
GATCCTAGATTTCAAGCCTCTTCATAAACCCAATGGCTTTATAACCTTACCACAGTTGGGCAACTGTGAAAAGATGTCAC
TGTCTTCCAAAGTGTCCCTACCCCTATCTCTGCATTAAGCAACATCAAATCGCTCTTCTTCCCCAAAATTGACTCTGATG
ACAGCAATCAGAAGAAAGCCAAGCTGGCAAGCACTTTCCATAGCATGTTCTGCCTCCGCAATGGCACATTCCAGAATTCC
CTAAAGCCTTTCACCCAAAGCAGTGCCAGTGACCTCAATGCACATTGTACTCTTGGGCTTCAGCTTTGAACTTAGACAAT
GGCACAGAGATGCCAACTCTGGCATCTTCACTGATGCCATCCCTCTCTGTTTGTCTGTGTGCACAGAGGAATCATCTTCC
AAATTGGTCAGCTCTTCAAACTTCTCAGTGTCACAAGTTCCTGACATGCCCAGCTGTCCCCAGGCCTATTCTGAACTGCA
GATGCTGTCCCCCAGTGAGTGACAGTATGTGGAGATAGTAGTCGGCATGGGTTATTTGTATGAGTGTGTCCTGAAAGTCA
TGAAAAAGAAAGAGGAGAACACTGAGCAGATTCCCGATTATCTCTTTGGCACAATGGACAGCTTTGTGAGAAGGGCTTCA
ACACCCTTTTAGTGGAAGAGGCTCTGGAAATGCACCATTGTTCACAAAAAAAG

Alignment

ORF - retro_tsyr_1908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.75 %
• Parental protein coverage: 64.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LLDSNLPRGGSGSVLQDEEVLASLERATLDFKPLHKPNGFITLPQLGNCEKMSLSSKVSLP-PIPAVSNI
          LLD.NL.R.GSGSVL..EE.LASLE.A.LDFKPLHKPNGFITLPQLGNCEKMSLSSKVSLP.PI.A.SNI
Retrocopy LLDNNLSRRGSGSVL*EEENLASLEWAILDFKPLHKPNGFITLPQLGNCEKMSLSSKVSLP<PISALSNI

Parental  KSLSFPKLDSDDSNQKTAKLASTFHSTSCLRNGTFQNSLKPFTQSSASDLNAHCTLGL-SALNLDNGTEM
          KSL.FPK.DSDDSNQK.AKLASTFHS..CLRNGTFQNSLKPFTQSSASDLNAHCTLGL.SALNLDNGTEM
Retrocopy KSLFFPKIDSDDSNQKKAKLASTFHSMFCLRNGTFQNSLKPFTQSSASDLNAHCTLGL<SALNLDNGTEM

Parental  PTLASSLMPSLSV-LSVCTEESLPN-VTPPNFAMSQVPNMPSCPQAYPELQTLSPSERQCVETVVNMGYS
          PTLASSLMPSLSV.LSVCTEES....V...NF..SQVP.MPSCPQAY.ELQ.LSPSE.Q.VE.VV.MGY.
Retrocopy PTLASSLMPSLSV<LSVCTEESSSKLVSSSNFSVSQVPDMPSCPQAYSELQMLSPSE*QYVEIVVGMGYL

Parental  YECVLRAMKKKGENIEQILDYLFA-H-GQLCEKGFDPLLVEEALEMHQCSEEK
          YECVL..MKKK.EN.EQI.DYLF..H.GQLCEKGF..LLVEEALEMH.CS..K
Retrocopy YECVLKVMKKKEENTEQIPDYLFG<HNGQLCEKGFNTLLVEEALEMHHCSQKK

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_1908 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.

---

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,