RetrogeneDB ID: retro_tsyr_582

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_143287:3450..4183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UAP1
• Ensembl ID: ENSTSYG00000002725
• Aliases: None
• Description: UDP-N-acteylglucosamine pyrophosphorylase 1 [Source:HGNC Symbol;Acc:12457]

Sequence

>retro_tsyr_582
TATATAACGACCAGTGGCAGAACAATAGAATCTACAAAGGAATTCTTCACCAGCCACAAGTACTTTGGTTTAAAACAAGA
GAATGTAATCTTTTTCCAGCAAGGAATGCTGCCTGCTGTCAGTTTTGATGGAAAAATTATTTTGGAAGAGAAGAGCAAAA
TTTCTATGACTCCAGAAATGGCAATGGTGGTCTTTATGAAGCTCTTGCAGCCCAGAATATTGTGGAGGATATAGAGCAAA
GAGGCATCTGGAGCATTCATGTCTATTGTGTTGACAGTATATTAGTAAAAGTGCAGACCCAGGGTTCATTGGACTTTGCA
TTCAGAAAGAAGCAGACTGTGGAATAAAGGTGGTAGAGAAAACGAACCCTACAGAACCAGTGGTTTGCTGAGTGGATGGA
GTTTACCAGGTGGTAGAATATAGTGAGATTTTCCTGGCAACAGCTCAGAAATGAAGCTTAGATGGACGACTGCTGTTCGG
TGCAGGAACATTGCCAACCATTTCTTTACCATACCATTTCTGAGCGATGTCATCAATATTTATGAATCCAGTTGCTGCAC
CATGTAACTCTAGAGAAGATTTCTTATGCGGATTCCCCAAGGGCAATTAAACCAGACAAACCAAATGGAATAAAGATGGA
AAAATTTGTCTTTGACACCTTCCAGTTCACAAAGCAATTTGTGCTATTGGAAGTATTATGGGAAGACGAATTTTCTCACT
GAAGAATGTAGAC

Alignment

ORF - retro_tsyr_582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.38 %
• Parental protein coverage: 85.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YIMTSGRTMESTKDFFTKHKYFGLKQENVIFFQQGMLPAMSFDGK-IILE-EKSKIAMAPDGNGGLYRAL
          YI.TSGRT.ESTK.FFT.HKYFGLKQENVIFFQQGMLPA.SFDGK.I..E.E.........GNGGLY.AL
Retrocopy YITTSGRTIESTKEFFTSHKYFGLKQENVIFFQQGMLPAVSFDGKIILEE<EEQNFYDSRNGNGGLYEAL

Parental  AAQNIVEDMEQRGIWSIHVYCVDNILV-KRADPR-IGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVY
          AAQNIVED.EQRGIWSIHVYCVD.ILV.K.ADP..IG.CIQK.ADCG.KVVEKTNPTEP..VVC.VDGVY
Retrocopy AAQNIVEDIEQRGIWSIHVYCVDSILV<KSADPGFIGLCIQKEADCGIKVVEKTNPTEP--VVC*VDGVY

Parental  QVVEYSEISLATAQKRSSDGRLLFNAG-NIANHFFTVPFLRDVVNIYEP-QLQHHVAQKKIPYVDSQGQL
          QVVEYSEI.LATAQK.S.DGRLLF.AG.NIANHFFT.PFL.DV.NIYE..QL.HHV...KI.Y.DS....
Retrocopy QVVEYSEIFLATAQK*SLDGRLLFGAG<NIANHFFTIPFLSDVINIYES<QLLHHVTLEKISYADSP-RA

Parental  IKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFS-PLKNAD
          IKPDKPNGIKMEKFVFD.FQF.K.FV..EVL.EDEFS..LKN.D
Retrocopy IKPDKPNGIKMEKFVFDTFQFTKQFVLLEVLWEDEFS<SLKNVD

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_582 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004264	1 retrocopy	retro_cjac_2537,
Cavia porcellus	ENSCPOG00000004568	5 retrocopies	retro_cpor_1186, retro_cpor_1187, retro_cpor_1188, retro_cpor_1189, retro_cpor_511,
Dasypus novemcinctus	ENSDNOG00000024661	1 retrocopy	retro_dnov_1035,
Macaca mulatta	ENSMMUG00000019514	1 retrocopy	retro_mmul_1238,
Rattus norvegicus	ENSRNOG00000002926	1 retrocopy	retro_rnor_2277,
Tarsius syrichta	ENSTSYG00000002725	3 retrocopies	retro_tsyr_121, retro_tsyr_390, retro_tsyr_582 ,