RetrogeneDB ID: retro_ogar_2773

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873663.1:3382284..3383148(+)
• Located in intron of: ENSOGAG00000025082

Retrocopy information

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

Parental gene information

• Parental gene symbol: OXCT1
• Ensembl ID: ENSOGAG00000009909
• Aliases: None
• Description: 3-oxoacid CoA transferase 1 [Source:HGNC Symbol;Acc:8527]

Sequence

>retro_ogar_2773
ATGGCCACGCGGCGGCTCCTGGCGGTGGTGCTTGGACGCTGTGTCCCCACCAGCCGCGCGGTGACCGCGCTGTCCCAGGG
CTGCGTCCGGCGCCGTTTTGCCACCAGCTCCCGTCCATGCGCCAAATTCTACACGGACCCTGTGGATATGGTGAAGGACA
TCTCCGATGGGGCCACCATCATGGTCGGGGGCTTCGGGCTGTGCGGCATCCCCGAGAACCTGATCGGGGCACTGCTGCAG
ACCGGCGTGAAGGACCTGAAGGTGGTGAGCAGCAACGTGGGCGTGGACGACTTCGGCCTGGGCCTCTTGATGGCCACCAA
GCAGATCCGCCGCATCGTCTGCTCCTACGTGGGCGAAAACAGGCTGTGCGAGGAGCAGTACCTGGCCGGCGAGCTGGAGC
TGGAGCTGACGCCGCAGGGCACCCTGGCCGAGCGCATCCGGGCGGGGGGTGCCGGGGTGCCCGCCTTCTACACACCCACG
GGGTACGGGACCCTGGTGCAGGAGGGGGGCTCCCCCATCAGGTACTACCCCGACGGCCACCTGGCCATCATGAGCCAGCC
GCGGGAGGTGCGTGAGATCGGAGGCCAGCACTACCTGCTGGAGCACGCCATCAGGGCGGACTTCGCCCTGGTCAAAGGCT
GGAAGGCCGACCGCATGGGCAACGTGATCTTCAGGGGGAGTGCCAGGAATTTCAACGTGCCCATGTGCAAAGCTGCAAAT
ATCACAGCCGTGGAGGTGGAAGAGATAGTGGATGTGGGGACTTTCCCCCCGGAGGACATCCACGTTCCTAGCATTTATGT
AGATCGCGTGATAAAGGGGGGAAATTTTGAGAAAAGAATTGAGCGTTTAAGGTTCCAGGAGGAA

Alignment

ORF - retro_ogar_2773 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.79 %
• Parental protein coverage: 55.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAFKFLSPGLRLCTSARGFKGAWSQGCVCY-FSTSSHRLTKFYTDPVEAVKDIPDGARILVGGFGLCGI
          MA....L...L..C........A.SQGCV...F.TSS....KFYTDPV..VKDI.DGA.I.VGGFGLCGI
Retrocopy MATRRLLAVVLGRCVPTSRAVTALSQGCVRRRFATSSRPCAKFYTDPVDMVKDISDGATIMVGGFGLCGI

Parental  PENLIGALLKTGVKGLTAVSNNAGVDNFGLGLLLQSKQIKRMISSYVGENVEFERQYLAGELEVELTPQG
          PENLIGALL.TGVK.L..VS.N.GVD.FGLGLL...KQI.R...SYVGEN...E.QYLAGELE.ELTPQG
Retrocopy PENLIGALLQTGVKDLKVVSSNVGVDDFGLGLLMATKQIRRIVCSYVGENRLCEEQYLAGELELELTPQG

Parental  TLAERIRAGGAGVPAFYTSTGYGTLVQEGGAPIKYNKDGSVAIASKPREVREFNGQHFIMEEAITGDFAL
          TLAERIRAGGAGVPAFYT.TGYGTLVQEGG.PI.Y..DG..AI.S.PREVRE..GQH...E.AI..DFAL
Retrocopy TLAERIRAGGAGVPAFYTPTGYGTLVQEGGSPIRYYPDGHLAIMSQPREVREIGGQHYLLEHAIRADFAL

Parental  VKAWKADRAGNVIFRKSARNFNLPMCKAAEITVVEVEEIVDIGTFAPEDIHIPQIYVHRLIKGEKYEKRI
          VK.WKADR.GNVIFR.SARNFN.PMCKAA.IT.VEVEEIVD.GTF.PEDIH.P.IYV.R.IKG...EKRI
Retrocopy VKGWKADRMGNVIFRGSARNFNVPMCKAANITAVEVEEIVDVGTFPPEDIHVPSIYVDRVIKGGNFEKRI

Parental  ERLSIRKD
          ERL.....
Retrocopy ERLRFQEE

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_2773 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033186	2 retrocopies	retro_btau_1243, retro_btau_1302,
Dipodomys ordii	ENSDORG00000016318	1 retrocopy	retro_dord_282,
Equus caballus	ENSECAG00000018312	1 retrocopy	retro_ecab_511,
Homo sapiens	ENSG00000083720	1 retrocopy	retro_hsap_14,
Gorilla gorilla	ENSGGOG00000025087	1 retrocopy	retro_ggor_378,
Myotis lucifugus	ENSMLUG00000009431	1 retrocopy	retro_mluc_194,
Nomascus leucogenys	ENSNLEG00000016656	1 retrocopy	retro_nleu_2438,
Oryctolagus cuniculus	ENSOCUG00000009231	1 retrocopy	retro_ocun_672,
Otolemur garnettii	ENSOGAG00000009909	2 retrocopies	retro_ogar_2773 , retro_ogar_2781,
Pongo abelii	ENSPPYG00000015428	2 retrocopies	retro_pabe_336, retro_pabe_478,
Pan troglodytes	ENSPTRG00000016829	1 retrocopy	retro_ptro_140,
Rattus norvegicus	ENSRNOG00000043094	2 retrocopies	retro_rnor_2177, retro_rnor_2256,
Ictidomys tridecemlineatus	ENSSTOG00000008271	1 retrocopy	retro_itri_747,
Tarsius syrichta	ENSTSYG00000013641	1 retrocopy	retro_tsyr_1455,
Tursiops truncatus	ENSTTRG00000004331	1 retrocopy	retro_ttru_875,
Vicugna pacos	ENSVPAG00000002550	1 retrocopy	retro_vpac_556,