RetrogeneDB ID: retro_ogar_518

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873522.1:29930838..29931601(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000030072
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPIA
• Ensembl ID: ENSOGAG00000034178
• Aliases: None
• Description: ribose 5-phosphate isomerase A [Source:HGNC Symbol;Acc:10297]

Sequence

>retro_ogar_518
GGGACCCTGGACGGTGCTGGAGGCACAAGCACCAGCGGTGGGGACTGCGGCAGCGTCCACCCGGCCCCCTCCACGGCAGA
GAAGCTGGCTGGCCACGCGGCGGAGGAGAACCATGTGAGGAATAAGCAAGTGCTGGGAATGGGAAATGGTTCTACAATTG
TCCTTGCTGGGCAGCGAATAGCTGAAAGAGTGAAGCAAGAGAACCTGAACCTCGTCTGCATTCCCACCTCCTTCCAGGCC
CATCCGCTCACCCTGCAGTACAACTTCCCGCTCAGTGACCGTATCAACACAGAGGCTGACCTCACCGGCGATGGTGCTGA
TGCAGTAGATGCTGATCTCAATCTCGTCAAGGGTGGTGGAGGCTGCCTGCCCCAGGATAAGACTGTGGCTGGCTGTGCCA
GTCCCCTCATTGTGATGGCTGATTTCAGGAAGGATTCAAAGAACCTTGGAGATCAGTGGCACGAGGGAATCCCCACGGAT
CTCTGTAGGTCATCAATGGCCTGCATCCCAGTAAGCCGAGTTGTGAGCCAGAAGTTTGAGGGTGCAGTTGAACTCCAAAT
GGCTGTTAACAAGGGAGGTCCCGTGGTGGCAGATAATGGGAATTTTATTTTGGATTGGAAGGTTGACTGGGTACACAAAT
GGAGTGAAGCTTTTAAAGTGATTCCAGGTGTGGTGGACACAGGTCTATTCTATCAACACCGCTGAGAGAGTTTCCTTCCG
GATGCAGGATGGCTCAGAGAACATGAAGGAGAAGCCTGTCTCT

Alignment

ORF - retro_ogar_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.58 %
• Parental protein coverage: 82.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSASTSGGDSDSVCPALSTMSKAEEAKKLAGRAAVENHVRNNQVLGIGSGSTIVHAVQRIAERVKQENLN
          G.....GG.S.S.....S.......A.KLAG.AA.ENHVRN.QVLG.G.GSTIV.A.QRIAERVKQENLN
Retrocopy GTLDGAGGTSTSGGDCGSVHPAPSTAEKLAGHAAEENHVRNKQVLGMGNGSTIVLAGQRIAERVKQENLN

Parental  LVCIPTSFQARQLILQHGLTLSDLDRHPEIDLAIDGADEVDADLNLIKGGGHRGCLTQEKIVAGYASRFI
          LVCIPTSFQA..L.LQ....LSD.....E.DL..DGAD.VDADLNL.KGGG..GCL.Q.K.VAG.AS..I
Retrocopy LVCIPTSFQAHPLTLQYNFPLSD-RINTEADLTGDGADAVDADLNLVKGGG--GCLPQDKTVAGCASPLI

Parental  VIADFRKDSKNLGDQWHKGIPIEVI--PMAYVPVSRAVSQKFGGAVELRMAVNKAGPVVTDNGNFILDWK
          V.ADFRKDSKNLGDQWH.GIP.......MA..PVSR.VSQKF.GAVEL.MAVNK.GPVV.DNGNFILDWK
Retrocopy VMADFRKDSKNLGDQWHEGIPTDLCRSSMACIPVSRVVSQKFEGAVELQMAVNKGGPVVADNGNFILDWK

Parental  FDRVHKWSEVNTAIKMIPGVVDTGLF-INMAERVYFGMQDGSVNMREKPFS
          .D.VHKWSE...A.K.IPGVVDTGLF.IN.AERV.F.MQDGS.NM.EKP.S
Retrocopy VDWVHKWSE---AFKVIPGVVDTGLF>INTAERVSFRMQDGSENMKEKPVS

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_518 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.

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002866	1 retrocopy	retro_btau_1373,
Equus caballus	ENSECAG00000011754	1 retrocopy	retro_ecab_645,
Macropus eugenii	ENSMEUG00000008256	1 retrocopy	retro_meug_1506,
Microcebus murinus	ENSMICG00000006462	1 retrocopy	retro_mmur_722,
Myotis lucifugus	ENSMLUG00000005384	1 retrocopy	retro_mluc_1129,
Monodelphis domestica	ENSMODG00000009649	1 retrocopy	retro_mdom_320,
Oryctolagus cuniculus	ENSOCUG00000006840	3 retrocopies	retro_ocun_1541, retro_ocun_1708, retro_ocun_1709,
Otolemur garnettii	ENSOGAG00000034178	2 retrocopies	retro_ogar_1218, retro_ogar_518 ,
Tarsius syrichta	ENSTSYG00000006406	8 retrocopies	retro_tsyr_1081, retro_tsyr_1088, retro_tsyr_1902, retro_tsyr_2028, retro_tsyr_393, retro_tsyr_709, retro_tsyr_725, retro_tsyr_994,
Tursiops truncatus	ENSTTRG00000000876	2 retrocopies	retro_ttru_1175, retro_ttru_799,