RetrogeneDB ID: retro_tsyr_121

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_3255:191389..192078(+)
• Located in intron of: ENSTSYG00000007470

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_121
AATGGTGGTCTTTACTGAGTTCTTGCAACCCAGAATATTGTGGAAGATATGAAGCAAAGAGGCATCTGGAGCATTCACGT
CTATTGTGTTGACAAAATAATAGTAAAAATGGCAGAACCATGGTTCATTGGATTTTGCATTCAGAAAGGAGCAGACTATG
GAGCCAAGGTAGTAGAGAAAACGAACCCTATAGAGCCAGTAAGAGTGGCTTGCCGAGTGGATGGAGTTTACCAAGTGGTA
GAATAAAGTGAGATTTCCCTGACAGCAGCTCAAAAATGAAGCTCAGCTGGACGACTGCTGTTCAATGTAGGGAACGTTGG
CAACTGTTTTCCCACTGTACAGTTTCTGAGAGATGTTGTCAATATTTATGAACGTCAGCTGCAGCACTATGTGGCTTAAA
GAAGATTCCTTATATGGATTCCCAACAACGGTTAATTAAGCCAGACAAACCAAATGGAATAAAGATGGAAAAATTTGTCT
TTGACATCTTCCAGTTCACAAAGAAGTTTGTGGTATATGAAGTACTATGGGAAGATGAATTTTCCCCGTTGAAGTATGCA
GACAGTCAGAATGGTAAGGACAACCCTACTACTGCAAGGCATGCCTTGATGTCCATTCATCATTGCTGGATCCTCAATGC
AGGGGGCTACTTCATAGATGAACATGACTCTTGCCTTCCAGCAATTCCC

Alignment

ORF - retro_tsyr_121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.25 %
• Parental protein coverage: 79.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKRADPR-IGFCIQKGADCGAKVVEKTNPTEPVGVV
          NGGLY..LA.QNIVEDM.QRGIWSIHVYCVD.I.VK.A.P..IGFCIQKGAD.GAKVVEKTNP.EPV.V.
Retrocopy NGGLY*VLATQNIVEDMKQRGIWSIHVYCVDKIIVKMAEPWFIGFCIQKGADYGAKVVEKTNPIEPVRVA

Parental  CRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLRDVVNIYEPQLQHHVA-QKKIPYV
          CRVDGVYQVVE.SEISL..AQK.SS.GRLLFN.GN..N.F.TV.FLRDVVNIYE.QLQH.VA..KKIPY.
Retrocopy CRVDGVYQVVE*SEISLTAAQK*SSAGRLLFNVGNVGNCFPTVQFLRDVVNIYERQLQHYVA<LKKIPYM

Parental  DSQGQLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALMSLHHC
          DSQ..LIKPDKPNGIKMEKFVFDIFQF.KKFVVYEVL.EDEFSPLK.ADSQNGKDNPTTARHALMS.HHC
Retrocopy DSQQRLIKPDKPNGIKMEKFVFDIFQFTKKFVVYEVLWEDEFSPLKYADSQNGKDNPTTARHALMSIHHC

Parental  WVLNAGGHFIDENGSRLPAIP
          W.LNAGG.FIDE..S.LPAIP
Retrocopy WILNAGGYFIDEHDSCLPAIP

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_121 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 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,