RetrogeneDB ID: retro_tsyr_2170

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_98769:1263..1945(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSTSYG00000010497
• Aliases: None
• Description: phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase [Source:HGNC Symbol;Acc:8587]

Sequence

>retro_tsyr_2170
ATAACCACCAAAGAAATTGTTCTTGCTGATGTGATTAATAATGATTCCTGGAGACTCTGGCCATCAGGAGATCGAAACCA
ACAGAAAGACAAACAGACTTACTGGGATCTCAAAGACGTAACTCCTGAAGGGCTACAGATGGTAAAGAAAAACTTTGAGT
GGGTTGCAGAGAGAGTAGAGTTGCTTTTGGAATCAGAAAGCCAATTCAGGGTTGTGATATTGATGGACTCTACTTTTGAT
CTCAGTCACTGAAAAAATCTAGAAGGCCTGTGACAATTTTGGCATTCCGTGTGAACTACAGGTAACATCTGCCCACAAAG
GACCAGATGAAACTCTGAGGATTAAGGCTGAGTATGAAGGGGATGGCATTCCTACTGTGTTTGTGGCAGTGGCAGGCAGA
AGCAATGGTTTGGAACCAGTGATATCTGGGAACACTGCATATCCACTTATCAGTTGTCCCCCTATTACACAAGACTGGGG
AGCTCAGGATGTGTGGTCCTCTCTTCGACTACCCCATGGTCTTCACTGTTCAACTATACTTTCTCCAGAAGGATCAGCTC
AGTTTGCTGCTCAGATATTTGGATTAAGCAACAATTTGCTATGGGGCAAACTGTGAGCAAGCATTTTGAACACATGGATT
TCCTTGAAGCAAGCTGACAAGAAAATCAGACAAAGTAATTTA

Alignment

ORF - retro_tsyr_2170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.59 %
• Parental protein coverage: 54.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTTKEIVLADVIDNDSWRLWPSGDRSQQKDKQSYRDLKEVTPEGLQMVKKNFEWVAERVELLLKSESQCR
          .TTKEIVLADVI.NDSWRLWPSGDR.QQKDKQ.Y.DLK.VTPEGLQMVKKNFEWVAERVELLL.SESQ.R
Retrocopy ITTKEIVLADVINNDSWRLWPSGDRNQQKDKQTYWDLKDVTPEGLQMVKKNFEWVAERVELLLESESQFR

Parental  VVVLMGSTSD-LSHCEKIKKACGNFGIPCELRVTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNGLG
          .VV.........S..EKI.KAC.NFGIPCEL.VTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNGL.
Retrocopy -VVILMDSTF>ISVTEKI*KACDNFGIPCELQVTSAHKGPDETLRIKAEYEGDGIPTVFVAVAGRSNGLE

Parental  PVMSGNTAYPVISCPPITPDWGAQDVWSSLRLPSGLGCSTILSPEGSAQFAAQIFGLNNHLIWGKLRASI
          PV.SGNTAYP.ISCPPIT.DWGAQDVWSSLRLP.GL.CSTILSPEGSAQFAAQIFGL.N.L.WGKL.ASI
Retrocopy PVISGNTAYPLISCPPITQDWGAQDVWSSLRLPHGLHCSTILSPEGSAQFAAQIFGLSNNLLWGKL*ASI

Parental  LNTWISLKQADKKIRQSNL
          LNTWISLKQADKKIRQSNL
Retrocopy LNTWISLKQADKKIRQSNL

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_2170 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 15 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010577	1 retrocopy	retro_btau_508,
Cavia porcellus	ENSCPOG00000010749	1 retrocopy	retro_cpor_969,
Dasypus novemcinctus	ENSDNOG00000013413	1 retrocopy	retro_dnov_284,
Echinops telfairi	ENSETEG00000015242	2 retrocopies	retro_etel_1918, retro_etel_341,
Homo sapiens	ENSG00000128050	3 retrocopies	retro_hsap_3802, retro_hsap_3915, retro_hsap_3927,
Gorilla gorilla	ENSGGOG00000024392	1 retrocopy	retro_ggor_2643,
Mus musculus	ENSMUSG00000029247	6 retrocopies	retro_mmus_1748, retro_mmus_2750, retro_mmus_2858, retro_mmus_3126, retro_mmus_653, retro_mmus_971,
Nomascus leucogenys	ENSNLEG00000008786	2 retrocopies	retro_nleu_1274, retro_nleu_2156,
Otolemur garnettii	ENSOGAG00000003575	2 retrocopies	retro_ogar_2138, retro_ogar_865,
Procavia capensis	ENSPCAG00000008531	1 retrocopy	retro_pcap_172,
Pan troglodytes	ENSPTRG00000016081	2 retrocopies	retro_ptro_2662, retro_ptro_2670,
Rattus norvegicus	ENSRNOG00000002101	3 retrocopies	retro_rnor_1891, retro_rnor_2768, retro_rnor_804,
Tupaia belangeri	ENSTBEG00000006751	1 retrocopy	retro_tbel_3697,
Tarsius syrichta	ENSTSYG00000010497	2 retrocopies	retro_tsyr_2170 , retro_tsyr_329,
Drosophila melanogaster	FBgn0020513	1 retrocopy	retro_dmel_82,