RetrogeneDB ID: retro_ogar_3439

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873838.1:10661..11427(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3A2
• Ensembl ID: ENSOGAG00000033389
• Aliases: None
• Description: splicing factor 3a, subunit 2, 66kDa [Source:HGNC Symbol;Acc:10766]

Sequence

>retro_ogar_3439
AGACCTTCAGTCTGGCAGCTGGCCCTGGAAACCACTGACATCCCCAAGGACCCATATTTTATGAAAAACCACGTGGGTTC
ATATGAATGCATACTCTGCCTGACGCTTCACAACAAGGAGGGAAGCTATCTCGCACATACCCAAGGAAAGAAGCACCAAA
TCAACTTGGCTGGGGGAGCAGCCAAGAAGGCAGGTGAAGGAGGCCCCTGCCCAGTCTGTGCCTGAGGTCAAGGTGGAGGT
GAAGAAGTTGGTGAAGATTGGCCGCACAGGCTACAAAGTGACCAAGCAGAGGGGCTCAGAGATGGGCCAGCAGAGCCTTC
TCTTCCAGATCGACTACCCTGAGATTGCTGAGGGCATCATGCTCCGCCACCGATTCATGTGTGCCTATGAGCAGAGGATT
GAGCCCCTGGACCAGCGCTGGCAATATTTGCTAATGGCCGCAGAGTCCTATGAGACCATTGCCTTCAAGGTACCTAGCAG
AGAGATCAACAAGGCTGAAGGCAAGTTTTGGACTCACTGGAACAGGGAAACCAAGCAGTTTTTCCTCTAGTTCCACTTTA
AAGGGAGAAGCCCCCCAGCTGCACTCAGCCTTCCTGCTGGGCCTCCTGGGGTGAACCGGCCTCCACCCCTGCTGAAGAAT
GGGTTGCCTCCTTGGCCTCCATTGCCTGAGTCTTTGCCAACACCCCTGCATGGGGGCCTACACCTGCTTCCCATGTCCCC
CACCAGGCCTGGACCCTCAGGGCCCCCAGGACCTCTCCAACTGCCC

Alignment

ORF - retro_ogar_3439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.08 %
• Parental protein coverage: 54.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RERLRQLALETIDINKDPYFMKNHLGSYECKLCLTLHNNEGSYLAHTQGKKHQTNLARRAAKEAKEAPAQ
          R....QLALET.DI.KDPYFMKNH.GSYEC.LCLTLHN.EGSYLAHTQGKKHQ.NLA..AAK.A.E....
Retrocopy RPSVWQLALETTDIPKDPYFMKNHVGSYECILCLTLHNKEGSYLAHTQGKKHQINLAGGAAKKAGEGGPC

Parental  P-APEKVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLLFQIDYPEIAEGIMPRHRFMSAYEQRIEPPDRR
          P.....VKVEVKK.VKIGR.GYKVTKQR.SEMGQQSLLFQIDYPEIAEGIM.RHRFM.AYEQRIEP.D.R
Retrocopy P>SVPEVKVEVKKLVKIGRTGYKVTKQRGSEMGQQSLLFQIDYPEIAEGIMLRHRFMCAYEQRIEPLDQR

Parental  WQYLLMAAEPYETIAFKVPSREIDKAEGKFWTHWNRETKQFFLQFHFKMEKPPAPPSLPAGPPGVKRPPP
          WQYLLMAAE.YETIAFKVPSREI.KAEGKFWTHWNRETKQFFL.FHFK...PPA..SLPAGPPGV.RPPP
Retrocopy WQYLLMAAESYETIAFKVPSREINKAEGKFWTHWNRETKQFFL*FHFKGRSPPAALSLPAGPPGVNRPPP

Parental  PLMNGLPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPPQLP
          .L.NGLPP.PPLPESLP.P..GGL.L.PM.PT.P.PSGPPGP.QLP
Retrocopy LLKNGLPPWPPLPESLPTPLHGGLHLLPMSPTRPGPSGPPGPLQLP

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_3439 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013206	4 retrocopies	retro_cjac_1621, retro_cjac_2029, retro_cjac_3563, retro_cjac_3971,
Otolemur garnettii	ENSOGAG00000033389	2 retrocopies	retro_ogar_3423, retro_ogar_3439 ,
Rattus norvegicus	ENSRNOG00000019349	1 retrocopy	retro_rnor_2822,