RetrogeneDB ID: retro_ogar_2741

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873658.1:788116..788546(-)
• Located in intron of: ENSOGAG00000014021

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP1
• Ensembl ID: ENSOGAG00000012167
• Aliases: None
• Description: nipsnap homolog 1 (C. elegans) [Source:HGNC Symbol;Acc:7827]

Sequence

>retro_ogar_2741
GATCAAGCTCAAAACAACCAGGAGTACGTGGAGCTCTGAAAGGTGTGGAGCCAGATGCTGCGATCCAGGAGAAACCAGCT
GTTCCTTGAGTTCAGCTTGTGGAATGAGCCAGAGCCCAGAGCAGTTCCCATTTATAAACTGAGGACCTGCAAGCTCAAGC
CAGGAACTATGATCCAGTGGGGGAACAACTGGGCTGGGGCCATCAAGTACCAGCGGGAGAACCAGGAGGCAGTGGGCAGC
TTCTCCTCACAGATAGGAGAGCTCTACATGGTGTACCATCTCTGTGCCTATAAAGATCTGCAGTCTTGGAAAATACTCAA
AATGCTGCCTGAAGGAAGAGAGGCTGGGATGAAAAGTCTACTGGATAGAACCCTTGTTAGGACACATGGCGTCTGGGATC
AAGATGCCCTTGAAGATACGGCCTCTGCAG

Alignment

ORF - retro_ogar_2741 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 51.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKLKNNKEYLEFRKERSQMLLSRRNQLLLEFSFWNEPEPRAGPNIYELRTYKLKPGTMIEWGNNWARAIK
          ....NN.EY.E..K..SQML.SRRNQL.LEFS.WNEPEPRA.P.IY.LRT.KLKPGTMI.WGNNWA.AIK
Retrocopy DQAQNNQEYVEL*KVWSQMLRSRRNQLFLEFSLWNEPEPRAVP-IYKLRTCKLKPGTMIQWGNNWAGAIK

Parental  YRQENQEAVGGFFSQIGELYIVHHLWAYKDLQS-REETRNAAWRKRGWDE-NVYYTVPLVRHMESRIMIP
          Y..ENQEAVG.F.SQIGELY.V.HL.AYKDLQS..E.T.NAA.RKRGWDE..VY...PL..HM.S.I..P
Retrocopy YQRENQEAVGSFSSQIGELYMVYHLCAYKDLQS<LENTQNAA*RKRGWDE<KVYWIEPLLGHMASGIKMP

Parental  LKISPLQ
          LKI.PLQ
Retrocopy LKIRPLQ

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_2741 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012291	1 retrocopy	retro_cfam_2091,
Otolemur garnettii	ENSOGAG00000012167	1 retrocopy	retro_ogar_2741 ,
Pteropus vampyrus	ENSPVAG00000017876	1 retrocopy	retro_pvam_675,
Sus scrofa	ENSSSCG00000009988	1 retrocopy	retro_sscr_615,
Tupaia belangeri	ENSTBEG00000004614	3 retrocopies	retro_tbel_247, retro_tbel_4673, retro_tbel_968,