RetrogeneDB ID: retro_ogar_865

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873529.1:15824719..15825361(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAICS
• Ensembl ID: ENSOGAG00000003575
• Aliases: None
• Description: phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase [Source:HGNC Symbol;Acc:8587]

Sequence

>retro_ogar_865
GAAATACTGGAGGAATTCTGGTCATCCCAGAACTGTACACTGGTTGATATGAAGATTGAATTTGATATTGATGTAACCAC
CAAAGAAATTGTTCTTGCTAATGTTATTGATAATGATTCCTGGAGACTCTGGCCATCAGATGATCGAAGCCAACAGAAAG
ACAAACAGTGTTACTGAGACCTCAAAGAAGTAACTCCTGAAGGGCTCCAAATGGTGAAGAAAAACTTTGAGTGGGTTACA
GAAAGAGTAAAGTTTCTTTTGACACCAGAAAGTTAGTGCAGGGTTGTAGTATTGATGGGCTCTACATCTGATCTCGGTCA
CTGTGAGAAAATCAAGGCCTATGGAAGTTTTGGCATTCCTTGTGAACTTCAGATAACATCTGCCCATAAAGGACCAGATG
AAACTCTGAGGATTAAATCTGAATACAATGGGGTTGGAATTCCTACTGTATTCGTGACAGTGGCAGGCAGAAGCAATGGT
TTGGGATCAGTGCTGTCTGGGAACAGTGCATATCCAGTTATCAACTGTTTGCCCCTCACTATGGACTGGGGAGCTCAGGA
TGTGTGGTCTTCTCTTCCACTACCCAGTGGTCTGGGCTATTCAACCATACTTTATCCAGAGGGATCAGCTCAGTTTGCTG
CG

Alignment

ORF - retro_ogar_865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.07 %
• Parental protein coverage: 51.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EILEKSWSPQNCTLVDMKIEFGVDVTTKEIVLADVIDNDSWRLWPSGDRSQQKDKQCYRDLKEVTPEGLQ
          EILE..WS.QNCTLVDMKIEF..DVTTKEIVLA.VIDNDSWRLWPS.DRSQQKDKQCY.DLKEVTPEGLQ
Retrocopy EILEEFWSSQNCTLVDMKIEFDIDVTTKEIVLANVIDNDSWRLWPSDDRSQQKDKQCY*DLKEVTPEGLQ

Parental  MVKKNFEWVAERVEFLLTPESQCRVVVLMGSTSDLGHCEKIKKACGSFGIPCELRITSAHKGPDETLRIK
          MVKKNFEWV.ERV.FLLTPES.CRVVVLMGSTSDLGHCEKI.KA.GSFGIPCEL.ITSAHKGPDETLRIK
Retrocopy MVKKNFEWVTERVKFLLTPES*CRVVVLMGSTSDLGHCEKI-KAYGSFGIPCELQITSAHKGPDETLRIK

Parental  SEYEGDGIPTVFVAVAGRSNGLGPVLSGNTAYPVINCPPLTMDWGAQDVWSSLRLPSESIGLGCSTILSP
          SEY.G.GIPTVFV.VAGRSNGLG.VLSGN.AYPVINC.PLTMDWGAQDVWSSL.LPS...GLG.STIL.P
Retrocopy SEYNGVGIPTVFVTVAGRSNGLGSVLSGNSAYPVINCLPLTMDWGAQDVWSSLPLPS---GLGYSTILYP

Parental  EGSAQFAA
          EGSAQFAA
Retrocopy EGSAQFAA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_865 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 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,