RetrogeneDB ID: retro_ogar_621

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873524.1:15149678..15150434(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFFL
• Ensembl ID: ENSOGAG00000024777
• Aliases: None
• Description: ring finger and FYVE-like domain containing E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:24821]

Sequence

>retro_ogar_621
ATGTGGGCAACCTGCTACAACTGGTTCTGTCTGAATCGACAGTCCAAGGAAGGCCCACCACCCAGGGAGCCAGGACACAG
GGAGTTCCAACTTTGGGTATAGCTCTTTTCCTTCTCCAATAGACTTGATCTGAACCAAGCTGCAGGGCCTGTGGAGCCCC
CTTGGCAAACACAGCCAGGAAGCAGATCTGCCTGGATGGTGACAAAAATTTCTGCATGACCTGTCCAAGCCAAGAGGGGA
ATGGGCCCCACCTCTGCCTTCTCTGCCAACGGTTTGGAACCACAGCCTTTCAGCCGGAGGAGCTCATGAAGATGGTGAAG
GACTAGAGGGACTATCTCAGTCTCTATGACATCTCTACCAAAATGTGCCTGAAGAAAGAAGAGCTGGTGTTCTTGGAGCT
TGGCCAGCAGCCTACAATCTCCCGGGATGGACCTGGTTCCCCCACCCTTGTCCTTGGACTTCCCTGAGCAGCAGGCCTTC
CTTAGCCAGCTTCACACCAGCACAATGGCTCCGACTTCACCCAGCCCCTCTTCATCTGCACAAGCCACCTCTGTCCCTGA
GCCCAGGCTCAGGAGCATCACCAGGCCAATGGCCATGTGTCTCAGGACCACAAAAGTCCATCTACCTGGCGAACACAGCC
AGAGCACCTGCTGAGGACAATTCCCAGTCCACTGATTCAGAGGACAGCTTCATCTGAGTCGGAGGGCCTCCCTGTCTGAC
CTGACCTACCTAGAGGACATTGAAGCCCTGACTGTG

Alignment

ORF - retro_ogar_621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.69 %
• Parental protein coverage: 70.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MWATCCNWFCLDGQPDEGPPP-QGARTQAYSNPGYSSFPSP-TGSEPSCKGCGAHFANTARKQICLDCKK
          MWATC.NWFCL..Q..EGPPP.QGARTQ.....G...F....T.SEPSC..CGA..ANTARKQICLD..K
Retrocopy MWATCYNWFCLNRQSKEGPPP<QGARTQGVPTLGIALFLLQ*T*SEPSCRACGAPLANTARKQICLDGDK

Parental  NFCMTCSSQEGNGPRLCLLCQRFRATAFQREELMKMKVKDLRDYLSLHDISTETCREKEELVFLVLGQQP
          NFCMTC.SQEGNGP.LCLLCQRF..TAFQ.EELMKM.VKD.RDYLSL.DIST..C..KEELVFL.LGQQP
Retrocopy NFCMTCPSQEGNGPHLCLLCQRFGTTAFQPEELMKM-VKD*RDYLSLYDISTKMCLKKEELVFLELGQQP

Parental  IISQEDRTRAPT-LSPDFPEQQAFLSQLHTSMVPPTSPSASSSAQATSVPP-AQAPEHQQANGHVSQDY-
          .IS..D....PT.LS.DFPEQQAFLSQLHTS...PTSPS.SSSAQATSVP..AQA.EH.QANGHVSQD..
Retrocopy TISR-DGPGSPT>LSLDFPEQQAFLSQLHTSTMAPTSPSPSSSAQATSVPE<AQAQEHHQANGHVSQDH<

Parental  EESVYLESTARAPAEDETQSIDSEDSFV-PGRRASLSDLTDLEDIEGLTV
          ..S.YL..TARAPAED..QS.DSEDSF....RRASLSDLT.LEDIE.LTV
Retrocopy QKSIYLANTARAPAEDNSQSTDSEDSFI<LSRRASLSDLTYLEDIEALTV

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_621 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001950	2 retrocopies	retro_chof_1069, retro_chof_285,
Macropus eugenii	ENSMEUG00000012628	1 retrocopy	retro_meug_1745,
Otolemur garnettii	ENSOGAG00000024777	1 retrocopy	retro_ogar_621 ,
Ochotona princeps	ENSOPRG00000011769	1 retrocopy	retro_opri_385,