RetrogeneDB ID: retro_ogar_2158

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873597.1:9399853..9400541(+)
• Located in intron of: ENSOGAG00000010239

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF114
• Ensembl ID: ENSOGAG00000003953
• Aliases: None
• Description: ring finger protein 114 [Source:HGNC Symbol;Acc:13094]

Sequence

>retro_ogar_2158
AAGATGGCAGCACAACAGCAGGAGCTTGAGGGTGGTGTGCAGCAGGCCAGGTGGGTAGCGGAGGCCGACTCCCTAGGCCG
CTTCACGTGTCCAGTGTGCTTAGAGGTGTACAAGAAGCCTGTGCAGGTGCCCTGCAGACACATCTTTTGCTCTGCATGCC
TGCAGGAATGTCTGAAGCTGAAGAAACCTGTCTGTGGGGTCTGTTGCAGCGCTCTGGCACCTGGCATCTGAGCTGTGGAG
CTCAAGCTGCAGATTGAGAGCACAGAGACTTCTTGCTATGGCTGCCGTTAGAATTTTTTTTTATCCAAGATCCGGGCCCA
TGTGGCTACCTGTTCTAAATATCAGAATTACATCATGGAAGGTGTGAAAGCCACCACTAAGGATGTGTCCTTTCAGCCAA
GGAATGTCCCAAGTTGTTATACCTTTCCTTGTCCTTATTGTCCCGAGAAGAACTTTGACCAGGAAGGACTTGTGGATAAT
TGTAAACTATCCCACAGCAAGGATACCAGATCTGTGGTTTGTCCGATATGTGCCTCTATGCCCTAGGGAGACCCCCAACT
ACCACAGCACCAACTTCATAGAGCACATCCAGGACCAGCACCAATTTTCTTATGATACTTTTGTGGATTATGATGTTGAT
GAAGAGGACATGATGCATCAAGTGTTGCAGCATTCCATCACTGGCCAG

Alignment

ORF - retro_ogar_2158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMAAQQQELEGGAQRAGSAAEADPLGRFTCPVCLEVYEKPVQVPCGHVFCSACLQECLKPKKPVCGVCRS
          KMAAQQQELEGG.Q.A...AEAD.LGRFTCPVCLEVY.KPVQVPC.H.FCSACLQECLK.KKPVCGVC.S
Retrocopy KMAAQQQELEGGVQQARWVAEADSLGRFTCPVCLEVYKKPVQVPCRHIFCSACLQECLKLKKPVCGVCCS

Parental  ALAPGVRAVELERQIESTETSCHGCRKNFFLSKIRAHVATCSKYQNYIMEGVKATTKDVSLQPRNVPNRY
          ALAPG..AVEL..QIESTETSC.GCR.....SKIRAHVATCSKYQNYIMEGVKATTKDVS.QPRNVP..Y
Retrocopy ALAPGI*AVELKLQIESTETSCYGCR*XXXXSKIRAHVATCSKYQNYIMEGVKATTKDVSFQPRNVPSCY

Parental  TFPCPYCPEKNFDQEGLVEHCKLSHSKDTKSVVCPICASMPWGD-PNYRSANFIEHIQRRHQFSYDTFVD
          TFPCPYCPEKNFDQEGLV..CKLSHSKDT.SVVCPICASMP.GD.PNY.S.NFIEHIQ..HQFSYDTFVD
Retrocopy TFPCPYCPEKNFDQEGLVDNCKLSHSKDTRSVVCPICASMP*GD>PNYHSTNFIEHIQDQHQFSYDTFVD

Parental  YDVDEEDMMNQVLQRSIIDQ
          YDVDEEDMM.QVLQ.SI..Q
Retrocopy YDVDEEDMMHQVLQHSITGQ

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_2158 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 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009113	2 retrocopies	retro_dnov_1534, retro_dnov_1557,
Microcebus murinus	ENSMICG00000011155	1 retrocopy	retro_mmur_992,
Otolemur garnettii	ENSOGAG00000003953	3 retrocopies	retro_ogar_1149, retro_ogar_2158 , retro_ogar_2330,
Ochotona princeps	ENSOPRG00000004732	2 retrocopies	retro_opri_368, retro_opri_709,
Pteropus vampyrus	ENSPVAG00000004117	4 retrocopies	retro_pvam_1136, retro_pvam_1148, retro_pvam_1149, retro_pvam_1477,
Sarcophilus harrisii	ENSSHAG00000001827	1 retrocopy	retro_shar_193,