RetrogeneDB ID: retro_ogar_2227

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873604.1:7878436..7879109(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSOGAG00000006265
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_ogar_2227
GAGAAGCTGCCTTGTAATACTTTCAGTACCTTTGGAGTCATCTTGCAAACCCCCAAGATTATGCTGGACCCTAATACAGA
CAACTCTACGGGTTATGTTTTTATTAATTTTGCTTTGTTTGATGTTTTGTATGCAGCCACTGAGGCCATGAATGGGAAGT
ACCTTTGTAACTGCCTATCACTGTCCTATGCCTTCAAGGACTCTTAAGGATGAGTACCATGGCTCAGCAACTGAATGACT
TCTGGGAGCTCAGAACTTGCTCACCCAGGCTGACCTCCCCCACCAGCAGTTAGTACATGCACCTCCTCCACCTTCTGCTC
CCATTCCCATGGTATCATCATTGTGAGCTGGGCTTCCACCACCAGGCATACCTCCTCCAGGCTCCTTCCCACCCTCAGTG
TCACCTCCTAGAGCCTTCTCATCTGGGATACCTCCAGCCCCATATCCGCAACCTATGCCTCCTGGGGCTGGGGGACATGG
CCACCCATCAGCAGGAACCCCAAGAGTAGGACATCCGGGTCACAGACACTCACATCCTCACCCATTTCTACCACATGGGA
TGCCCCATCCAAGGATGTCTCTGATGCAGCTGGCATACCAAGGCCCTCATGGCTTAGGACACCCCCATGTAGGGACCCCA
GGCCCTGGGGCACAGTCACCATCTCTACCACCA

Alignment

ORF - retro_ogar_2227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.37 %
• Parental protein coverage: 53.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS
          EKL...TFS.FGVILQTPKIM.DP.T.NS.GY.FINFA.FD...AA.EAMNG.YLCN.....SYAFK.DS
Retrocopy EKLPCNTFSTFGVILQTPKIMLDPNTDNSTGYVFINFALFDVLYAATEAMNGKYLCNC-LSLSYAFK-DS

Parental  -KGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPG
          .K.E.HGSA.E.LL.AQN.L.QAD.PHQ....APPPPSAP.P.VSSL..GLPPPG.PPPGSFPP.V.PP.
Retrocopy >KDEYHGSATE*LLGAQNLLTQADLPHQQLVHAPPPPSAPIPMVSSL*AGLPPPGIPPPGSFPPSVSPPR

Parental  ALPPGIPPAMPPPPMPPGAGGHGPPSAGTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGH
          A...GIPPA..P.PMPPGAGGHG.PSAGTP..GHPGH.HSHPHPF.P.GMPHP.MS.MQLA..GPHGLGH
Retrocopy AFSSGIPPAPYPQPMPPGAGGHGHPSAGTPRVGHPGHRHSHPHPFLPHGMPHPRMSLMQLAYQGPHGLGH

Parental  PHAGPPGSGGQPPPRPP
          PH.G.PG.G.Q.P..PP
Retrocopy PHVGTPGPGAQSPSLPP

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_2227 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Felis catus	ENSFCAG00000010106	1 retrocopy	retro_fcat_1607,
Mus musculus	ENSMUSG00000068856	1 retrocopy	retro_mmus_1406,
Otolemur garnettii	ENSOGAG00000006265	3 retrocopies	retro_ogar_2227 , retro_ogar_2388, retro_ogar_2804,
Otolemur garnettii	ENSOGAG00000016857	1 retrocopy	retro_ogar_3103,