RetrogeneDB ID: retro_ogar_2388

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873618.1:1156288..1157513(-)
• 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_2388
ATGGCTGCCAGGCTGATCTCCGAGCAGAACCAGGATGCCACCATATACATGGGGGGTCTGGATGAGAAGGTTAGTGAACC
ACTGCTGTGGGAACTATTTCTTCAGGCTGGACCGGTAGTCAACACCCACGTGCCAAAGGATAGGGTCACAGGCCAGCACC
AAGGATATGGTTTTGTGGAATTCCTGAGCAAAGAAGATGCTGACTATGCCATTAAGATCATGAACATGATCAAACTCTAT
GGGAAACCAATATGTGTGAACAGGGCATCAGTTTACAACAAAAACCTGAATGTAGGGGCCAACATTTTCATTGGGAACCT
GGACCCAGAGAGTAATGAAAGCTGCTTTATGATACTTTCAGCACCTTTGAGTCATCTTACAACCCCCCCAAGATTATGTG
GGACTCTAACACAGGCAACTCCAAGGGTTATCCTTTTATTAATTTTATTTTGTTTGGTGCTTCAGATGCAGCAATTGAGG
CTATGAATGGTCAGTACCTTTGTAACCACCTAATCACTGTGTCTAATGCCTTCAAGAAGGACTCTTAAGGGTGAGTGCCA
TGGCTCAGTAGCTGAACAACTTCTGGCAGCTCAGAACTCACTCTCCCAGGCTGACAACTCCCATCAGCTATTTGCAGGTG
CACATCCTTCACCTTCTGCCCCTAATCTGGTGGTATCATCATTGGGATCTGGGCTCCCATGACCAGGCATGCCTCCTCCT
GGCTCCTTCCCAACTCCAGTGCCACCTCCTGGAACCGTCTCACCTGGGATACCCCCAGCCATGCCTCTGCCACCTATGCC
TTCCATGACTGAAAGACATGCCCCCCCCATCAGCAGGAACCCCAGGAGCAGGACATTCTAGTCACAGACCCTCACATCCT
CATCCATTTCCAAAGGGTCATCCAGTGATGGCTCAGATGTAACCGGCACACCATGGCCCTCATGGCTTAGGATACCCCCA
TGTGGGGCCCCCAGCCTCTTGGGGACAGCTAACACCTTGAACGCCTCATCCTAAACCTCCTGCAATGGGCATGCCCCCCA
CCCAAGGGCCTCCAATTGAGCCTCCCATGGGCCACCCAGGTCTTATGCCCCCACATGGTATGCATGGACCTCCTCCACTG
ATTTCCCCTCATGGATACACTGGCCGTCTATTACCCCCACCCTATGGCTACCAGAGGCGACCTCTCCCGGCCTCTAGTTC
CCCCTTGTAGCCTGCTCCACGGCCC

Alignment

ORF - retro_ogar_2388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.12 %
• Parental protein coverage: 96.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
          MAA..ISE.NQDAT.Y.GGLDEKVSEPLLWELFLQAGPVVNTH.PKDRVTGQHQGYGFVEFLS.EDADYA
Retrocopy MAARLISEQNQDATIYMGGLDEKVSEPLLWELFLQAGPVVNTHVPKDRVTGQHQGYGFVEFLSKEDADYA

Parental  IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDE-KLLYDTFSAFGVILQTPKIMRDPDTG
          IKIMNMIKLYGKPI.VN.AS..NKNL.VGANIFIGNLDPE..E.KLLYDTFS.F......PKIM.D..TG
Retrocopy IKIMNMIKLYGKPICVNRASVYNKNLNVGANIFIGNLDPESNE<KLLYDTFSTFESSYNPPKIMWDSNTG

Parental  NSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS-KGERHGSAAERLLAAQNPLSQADRPH
          NSKGY.FINF..F.ASDAAIEAMNGQYLCN..ITVS.AFKKDS.KGE.HGS.AE.LLAAQN.LSQAD..H
Retrocopy NSKGYPFINFILFGASDAAIEAMNGQYLCNHLITVSNAFKKDS>KGECHGSVAEQLLAAQNSLSQADNSH

Parental  QLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGH-GPPS
          QLFA.A.P.PSAPN.VVSSLGSGLP.PGMPPPGSFP.PVPPPG...PGIPPAMP.PPMP.....H....S
Retrocopy QLFAGAHPSPSAPNLVVSSLGSGLP*PGMPPPGSFPTPVPPPGTVSPGIPPAMPLPPMPSMTERH>XXXS

Parental  AGTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPP
          AGTPGAGH..H..SHPHPFP.G...HP.M.QM..AHHGPHGLG.PH.GPP.S.GQ..P..P....HP.PP
Retrocopy AGTPGAGHSSHRPSHPHPFPKG---HPVMAQM*PAHHGPHGLGYPHVGPPASWGQLTP*TP----HPKPP

Parental  PMGMPP-RGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGPLP----PPRPTPRP
          .MGMPP..GPP...PMGHPG.MPPHGM.GPPPL..PHGYTG...PPPYGYQR.PLP....P..P.PRP
Retrocopy AMGMPPTQGPPIEPPMGHPGLMPPHGMHGPPPLISPHGYTGRLLPPPYGYQRRPLPASSSPL*PAPRP

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_2388 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.

---

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,