RetrogeneDB ID: retro_tsyr_329

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_8374:123334..124158(+)
• 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_329
CTGAACATTGGTTAGAAAACTGTATTAGGGAAAGCAAAAGAAGTCTATGAATTGCTAGGTAGTCCAGGAAAAGTTCTTCT
GTAGTCCCAGGACCAAACTGCAGCAGAAAATGCAGTTAAAAAGAATCACCCGGAAGGAAAAGCTGCGATCTTAAATAAAA
CTAGCAGCTGTATCTTTCAGCTGTTGCAGGAAGCAGGCATCAAAACTGCTTTCACCAGAAAATGTGGGGAAACAGCTTTT
ATTGCACCCCAGCGTGAGATCATTCCAATCGAATGGGTTTGCTGAAGAATAGCAACTGGTTCTTTCTCAAAAAGAAATCC
TGGTGTCAAGGGAAGATATAAGTTTTACCCATCTCAAGTGGAGGTGTTTTTCAAGGAGGATGCCAGGAATGACCCACAGT
GGTCTGAGGAATAGCTCATTGCTGCAAAATTTTGTTTTGCTGGACTTGATACCCAGTCAAACTGAAGTGGGTATCATGAG
TCATGCTACATACACTGTTTCTGAAATACTGGAGAAATTCTGGTTGCCCAAGAACTGTACACTGGTTGATATGAAGATTG
AATTCGATGTTGATGTAACCACCAAAGAAATCGTTCTTGCTGATGTAATTGATAATGATTCCTGGACACTCTGGCCATCA
GGAGATTAAAGCCAACAGAAAGACAAACAGTCCTACTTGGGTCTCAAAGAAATAACTCCTGAAGGGCTGCAGATTAAAGG
AAAACATTGAGTGGGTTGCAGAGAGATTAGAGTTGCTTTTGAAATCAGAAAGTCAATGCAAGGTTGTGATGCTGATAGGG
TCTACTTTTGAGCTCAACCACTGT

Alignment

ORF - retro_tsyr_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.62 %
• Parental protein coverage: 65.63 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LNIGKKLYEGKTKEVYELLDSPGKVLLQSKDQITAGNAARRNHLEGKAAISNKITSWIFQLLQEAGIKTA
          LNIG.K...GK.KEVYELL.SPGKVLL.S.DQ..A.NA...NH.EGKAAI.NK..S.IFQLLQEAGIKTA
Retrocopy LNIG*KTVLGKAKEVYELLGSPGKVLL*SQDQTAAENAVKKNHPEGKAAILNKTSSCIFQLLQEAGIKTA

Parental  FTRKCGETAFIAPQCEMIPIEWVCRRIATGSFLKRNPGVKEGYKFYPPKVEMFFKDDANNDPQWSEEQLI
          FTRKCGETAFIAPQ.E.IPIEWVC.RIATGSF.KRNPGVK..YKFYP..VE.FFK.DA.NDPQWSEE.LI
Retrocopy FTRKCGETAFIAPQREIIPIEWVC*RIATGSFSKRNPGVKGRYKFYPSQVEVFFKEDARNDPQWSEE*LI

Parental  AAKFCFAGLDI-GQTEVDIMSHATQAIFEILEKSWLPQNCTLVDMKIEFGVDVTTKEIVLADVIDNDSWR
          AAKFCFAGLD...QTEV.IMSHAT....EILEK.WLP.NCTLVDMKIEF.VDVTTKEIVLADVIDNDSW.
Retrocopy AAKFCFAGLDT>SQTEVGIMSHATYTVSEILEKFWLPKNCTLVDMKIEFDVDVTTKEIVLADVIDNDSWT

Parental  LWPSGDRSQQKDKQSYRDLKEVTP-EGLQMVKKNFEWVAERVELLLKSESQCRVVVLMGSTSDLSHC
          LWPSGD.SQQKDKQSY..LKE.TP..G....K.N.EWVAER.ELLLKSESQC.VV.L.GST..L.HC
Retrocopy LWPSGD*SQQKDKQSYLGLKEITP>KGCRL-KENIEWVAERLELLLKSESQCKVVMLIGSTFELNHC

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_329 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,