RetrogeneDB ID: retro_ogar_1144

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873536.1:29581487..29582098(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSFL1C
• Ensembl ID: ENSOGAG00000002630
• Aliases: None
• Description: NSFL1 (p97) cofactor (p47) [Source:HGNC Symbol;Acc:15912]

Sequence

>retro_ogar_1144
TTTGCAGGGGTGGCTACTGCCTTGGGGCAGCACCAGAGGGAGAGTCTACCATTGCAGCAGGAGAAAGGAGGCTGCATTCC
AGCTGAGATTTTCATACAGCATGGGCTGTCTGGTAGAGTGGATTCAGGCTGGACAGTGGTGAACTCAGAAACTATCAAGA
CCCATCCAATGCCCAGTTTCTGGAGTCTATCCTAGAAGAGAGGTATCAGCAGAGCTGCAGAGGTCAGCTCACACTGGGCA
GGTGGGCATGGATATGGAGGCACAGTGGGAGGAGGACTTCATGAAGCCCACGGGAGCCTTCAGAGCCTTCACTGGAGAGG
GCTAGAAACTGGGCAGCACGGACCCCAGTTGTTGTGCACCAGTTTCCCAGCGCAACAGGCATAAAATAAAGCCAAATCCA
GCTCTTCTATCTTAACCAAGTCAGAGCCTTCTGCAAATATCCAAATTCAGCTTGCCGACAGTGGGGAGCTGGAGCAGAGC
TTTAACCACAGTGGCGGGGTCAGTGACATCTAACTGTCCACTGTGAATGCCAGCCAGCTACAGCTGCCACCCACTTTATT
CTCATAACTACCTTCCCAAAGAGCTAGACCCTGAATGAAGCCAGCTGGCTC

Alignment

ORF - retro_ogar_1144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.81 %
• Parental protein coverage: 55.68 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FAG-GGYRLGAAPEEESAYVAGERKQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLESI-RRGE
          FAG.GGY.LGAAPE.ES...AGER..HSS.D.H.....W.SGF.LD.GELR.YQDPSNAQFLESI..R.E
Retrocopy FAG<GGYCLGAAPEGESTIAAGERRLHSS*DFHTAWAVW*SGFRLDSGELRNYQDPSNAQFLESI<PRRE

Parental  VPAELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGST-APQVLNTSSPAQQAENEAKASSS
          V.AEL.R.AH.GQV..DME....EDF.KP.GAF.AFTGEG.KLGST..PQ.L.TS.PAQQA.N.AK.SSS
Retrocopy VSAELQRSAHTGQVGMDMEAQWEEDFMKPTGAFRAFTGEG*KLGST<GPQLLCTSFPAQQA*NKAKSSSS

Parental  ILINESEPTTNIQIRLADGGRLVQKFNHSHRISDIRLFIVDA-RPAMAATSFVLMTTFPNKELADESQTL
          IL...SEP..NIQI.LAD.G.L.Q.FNHS...SDI.L..V.A..PA.AAT.F.L.TTFP......E...L
Retrocopy IL-TKSEPSANIQIQLADSGELEQSFNHSGGVSDI*LSTVNA<QPATAATHFILITTFPKS*TLNEASWL

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_1144 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088833	1 retrocopy	retro_hsap_4050,
Gorilla gorilla	ENSGGOG00000013539	1 retrocopy	retro_ggor_2718,
Macropus eugenii	ENSMEUG00000003940	2 retrocopies	retro_meug_1890, retro_meug_605,
Macaca mulatta	ENSMMUG00000015994	1 retrocopy	retro_mmul_2337,
Mus musculus	ENSMUSG00000027455	1 retrocopy	retro_mmus_2565,
Nomascus leucogenys	ENSNLEG00000009341	1 retrocopy	retro_nleu_2800,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Otolemur garnettii	ENSOGAG00000002630	2 retrocopies	retro_ogar_1144 , retro_ogar_1609,
Pongo abelii	ENSPPYG00000010851	1 retrocopy	retro_pabe_3324,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,