RetrogeneDB ID: retro_ogar_2259

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873607.1:2679529..2680380(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000024458
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000010065
• Aliases: None
• Description: None

Sequence

>retro_ogar_2259
CCCTGGTTCTGCGATGCTGGGGCCGGGTACACCTGCTCAGTGTGGGGGAGGGTAAGGAGCAGGCAGCCGCAGGGCAGAAA
CGGAAGCAGGGGAGTGCCAGGGAACCGAGCGGGAAAGGAAGGAGAGAAAAAGATCCGCCAGGAGGGAGACACCCTCCTAG
GGCACTCCAGGCTCTCCGGGTCCACGGAGAGCAGTCCTGGGAAAGGAAGTCGAATGAGGCCAGTTAAAATTGATGCTCCA
GAATACATCCCCTAGGAGATGGCCCCGAGGCACCAGCAAAGGAAAAAATGAAATCCAAGAAGAAGGTAGAGCAGCCAGTC
ATGGAGGAGGTGGCTCTGAAAGGGAAGAAGAAGAAGAGGAAGAAAGACAGCGGGTAGCAGGAGACCCTTGGGAGGAGGAT
CCAGACCCAGACCTGGAGGTGGTGACGGAAAAGAAAGGGAACGTGGACGAGGAGCACACTGACCAGGGGAGGCGAAGGCC
TTGCGAGAAGAGACTGACCGTGAGTCGGGCAAAATGGAAACGTCTGAAACCAGCAAGTGACGGGAACCCAGTTTGGCCAG
TGGGATACTGCTGGTTTTGAAAATGAGGACCAGAAACTGAAATTTCTCAAACTTATGGGTGGCTTTAAAAATCTGTCCCC
TTCATTCAGCCAGCCCCCTAGCATGGCTGGAAGGCCCAACATGGCCCTCAACAGGAAGGCAGCTGACACTCTGCAGCAGA
ACCTGCAACGGGACTACGACCAGGCCATGAGCTGGAAGTACAGCCGAGGAGCTGGCCTTGGCTTCTCTAATGCTGCAGAC
GAAATCTTTTATATTGACAGAAACGCTTCTAAATCTATCAAGTTTGAAGAT

Alignment

ORF - retro_ogar_2259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.67 %
• Parental protein coverage: 62.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PWFCNAGDGYTCSVGR-EGKEQAAPGQKRKQGSAREPS-GKGKKKKKIYQEGDTLLGHSKLSRSTESSPR
          PWFC.AG.GYTCSV...EGKEQAA.GQKRKQGSAREPS.GK....KKI.QEGDTLLGHS.LS.STESSP.
Retrocopy PWFCDAGAGYTCSVWG<EGKEQAAAGQKRKQGSAREPS>GK-EGEKKIRQEGDTLLGHSRLSGSTESSPG

Parental  KGSRMKPVKIDAPEYIP-LGDGPKAPAKKKMKSKKKVEQPVMEEVALKRKKKKKRKKDSG-VVGDPWKED
          KGSRM.PVKIDAPEYIP.LGDGP.APAK.KMKSKKKVEQPVMEEVALK.KKKK.RKKDSG.V.GDPW.ED
Retrocopy KGSRMRPVKIDAPEYIP<LGDGPEAPAKEKMKSKKKVEQPVMEEVALKGKKKK-RKKDSG<VAGDPWEED

Parental  PDPDLEVVLEKKGNMDEAHIDQVRR-KALQEEIDRESGKTETSETRK-WTGTQFGQWDTAGFENEEQKVK
          PDPDLEVV.EKKGN.DE.H.DQ.RR.KAL.EE.DRESGK.ETSET.K..TGTQFGQWDTAGFENE.QK.K
Retrocopy PDPDLEVVTEKKGNVDEEHTDQGRR<KALREETDRESGKMETSETSK<VTGTQFGQWDTAGFENEDQKLK

Parental  FLKLMGGFKNLSPSFSRPPSMAGRPNMALNKKAADTLQQNLQRDYDRAMSWKYSRGAGLGFSNAADKIFY
          FLKLMGGFKNLSPSFS.PPSMAGRPNMALN.KAADTLQQNLQRDYD.AMSWKYSRGAGLGFSNAAD.IFY
Retrocopy FLKLMGGFKNLSPSFSQPPSMAGRPNMALNRKAADTLQQNLQRDYDQAMSWKYSRGAGLGFSNAADEIFY

Parental  IDRNASKSIKFED
          IDRNASKSIKFED
Retrocopy IDRNASKSIKFED

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_2259 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 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018032	2 retrocopies	retro_cfam_1557, retro_cfam_1763,
Callithrix jacchus	ENSCJAG00000009625	1 retrocopy	retro_cjac_3199,
Homo sapiens	ENSG00000103550	3 retrocopies	retro_hsap_3487, retro_hsap_4007, retro_hsap_979,
Gorilla gorilla	ENSGGOG00000005673	1 retrocopy	retro_ggor_2691,
Macaca mulatta	ENSMMUG00000002707	2 retrocopies	retro_mmul_1771, retro_mmul_798,
Nomascus leucogenys	ENSNLEG00000012496	2 retrocopies	retro_nleu_1618, retro_nleu_551,
Otolemur garnettii	ENSOGAG00000010065	4 retrocopies	retro_ogar_1115, retro_ogar_1480, retro_ogar_1481, retro_ogar_2259 ,
Pongo abelii	ENSPPYG00000007151	3 retrocopies	retro_pabe_3293, retro_pabe_828, retro_pabe_920,
Pan troglodytes	ENSPTRG00000007836	3 retrocopies	retro_ptro_2360, retro_ptro_767, retro_ptro_924,