RetrogeneDB ID: retro_ogar_2940

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873685.1:2234117..2234500(-)
• Located in intron of: ENSOGAG00000000659

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX24
• Ensembl ID: ENSOGAG00000005170
• Aliases: None
• Description: sorting nexin 24 [Source:HGNC Symbol;Acc:21533]

Sequence

>retro_ogar_2940
TTTCATGCTTTGCACAAAAAGCTTAAAAAATGTATAAAAACTCCAGGAATTCCTTCGAAACATGTTAGGAACTGGGCTCC
AAAGGTGTTAGAACAACGACGACAAGGTTTGGAAACATATTTATAGGCTGTCATTTTAGAAAATGAAGAACTCCCCAAAC
TGTTTCTTGATTTTCTAAATGTGCAACACTTGCCCTCTCTACCAAAGGCAGAAAGTTGTGGATCTTTTGACGAGACAGAA
TCTGAAGAGTCAAGCAAACTGTCCCACCAGCCCGTGCTGCTGGTCCTCGGGGATCCATACGTCTTGCCTGCAGCCAGCGA
TTTTCTGAATGTGGTTATTGAGGGAGTGCTCCATGGGACTTTTGCCCTCATCTGCAGCCCAAG

Alignment

ORF - retro_ogar_2940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 63.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FHALHKKLKKCIKTPEIPSKHVRNWVPKVLEQRRQGLETYLQAVILENEELPKLFLDFLNVRHLPSLPKA
          FHALHKKLKKCIKTP.IPSKHVRNW.PKVLEQRRQGLETYL.AVILENEELPKLFLDFLNV.HLPSLPKA
Retrocopy FHALHKKLKKCIKTPGIPSKHVRNWAPKVLEQRRQGLETYL*AVILENEELPKLFLDFLNVQHLPSLPKA

Parental  ESCGSFDETESEESSKLSHQPVLLFLRDPYVLPAASDFPNVVIEGVLHGI-FYPHLQPR
          ESCGSFDETESEESSKLSHQPVLL.L.DPYVLPAASDF.NVVIEGVLHG..F.PHLQP.
Retrocopy ESCGSFDETESEESSKLSHQPVLLVLGDPYVLPAASDFLNVVIEGVLHGT<FCPHLQPK

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_2940 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031069	1 retrocopy	retro_btau_640,
Choloepus hoffmanni	ENSCHOG00000006859	2 retrocopies	retro_chof_1841, retro_chof_544,
Dasypus novemcinctus	ENSDNOG00000019810	1 retrocopy	retro_dnov_261,
Echinops telfairi	ENSETEG00000010310	1 retrocopy	retro_etel_923,
Microcebus murinus	ENSMICG00000001708	1 retrocopy	retro_mmur_1043,
Myotis lucifugus	ENSMLUG00000009392	2 retrocopies	retro_mluc_1022, retro_mluc_2330,
Monodelphis domestica	ENSMODG00000013427	1 retrocopy	retro_mdom_1215,
Otolemur garnettii	ENSOGAG00000005170	2 retrocopies	retro_ogar_2940 , retro_ogar_975,
Sorex araneus	ENSSARG00000009785	1 retrocopy	retro_sara_99,
Sarcophilus harrisii	ENSSHAG00000011329	1 retrocopy	retro_shar_488,
Tarsius syrichta	ENSTSYG00000014395	2 retrocopies	retro_tsyr_1563, retro_tsyr_1691,