RetrogeneDB ID: retro_ogar_2804

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873665.1:1080234..1081490(-)
• 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_2804
ATGGCTGGCGGGCCGATCTCTGAGCAGAACCAGGATGCCACCGTATACGTGGGGGGTCTGGATAAGAAGGTTAGTGAACC
ATTGCTGTGGAAACTGTTTCTCCAGGCAGGACCAGTAGTCAACACCCACATGCCAAAGTGTAGAGTCACAGGCCAGCACC
AAGGATATGGTTTTGTGGAAGTCTTGAGTGAGAAGGATGCTGACTATGCCATTAAGATCATGAACATGATCAAACTCTAT
GGGAAACCAATACATGTGAAAAAGGCATCAGCTCACAACAAAAACCTGGATGTAGGGGCCAACATTTTCATTAGGAACCT
AGACCCAGAGATTGATGAGAAGCTGCTTTATGATACTTTCAGTGCCTTTGGAGTCATCTTACAAACCTCCAAGATTATGC
AGGACCCTGACACAGGCAACTCCAAAGGTTATGCTTTTATTAATTTTGCTTCGTTTGATGCTTTGGATGCAGCAATTGAG
GCTATGAATGGGCAGTACCTTTGTAACTGCCCTATCACTATGTCTTATGCCTTCAAGAAGGACTCAAAGGGGGAGCGCCA
TGGCTCAGCTGCTGAACGACTTCTGGCAGCTCAGAACCCACTCTCCCAGGCTGACCACCCCCATCAGCTGTTTACAGATG
CACCTCCTCCACCTTCTGCCCCCAATCCTGTGGTATCATCATTGGGATCTGGGTTTCCACTACCAGGCATGCCTCCTCCT
GGCTCCTTCGCACCCCCAGTGCCACCTCCTGGAGCCCTCCCACCTGGGATACCCCCAGCCATGCCTCCACCACCTATACC
TCCTGGGGCTGGGGGACATAGCCCCTGATCAGCAGGAAGCCCAGGAGCAGGACACTCATATCCTCACCCATTTCCTCCAG
GTGGGATTCCCCATCCAACGATGTCTCAGATACAACTGGCACACCATGTCCCCCATGGCTTAGGACACCACCATGTAGGA
CCCCCAGGTTCTGGGGGACAGCCACCACCTCGACCACCACCTGGAATGCCTCATCCTGGACTTCCTCCAATGGGCATGCT
CCCCAGAGGGCCTCCATTTGGGTCTCCCATGGATCATCCAGGTCCTATGCCCCTACATGGTATGCATGGACCTCCTCCAC
TGATGCCCCCTTGTGGATACCCTGGCCATCCATGCCCCCCACCCTATGCTACCAGAGGAGACCTCTCCCTCCACCTAGAC
CAACTCCCTGGCCTCCAGTTCCCCCTCATGACCTGCTCTGGGGCCCTCTGCCTCAG

Alignment

ORF - retro_ogar_2804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA
          MA.GPISE.NQDATVYVGGLD.KVSEPLLW.LFLQAGPVVNTHMPK.RVTGQHQGYGFVE.LSE.DADYA
Retrocopy MAGGPISEQNQDATVYVGGLDKKVSEPLLWKLFLQAGPVVNTHMPKCRVTGQHQGYGFVEVLSEKDADYA

Parental  IKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGN
          IKIMNMIKLYGKPI.V.KASAHNKNLDVGANIFI.NLDPEIDEKLLYDTFSAFGVILQT.KIM.DPDTGN
Retrocopy IKIMNMIKLYGKPIHVKKASAHNKNLDVGANIFIRNLDPEIDEKLLYDTFSAFGVILQTSKIMQDPDTGN

Parental  SKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQL
          SKGYAFINFASFDA.DAAIEAMNGQYLCN.PIT.SYAFKKDSKGERHGSAAERLLAAQNPLSQAD.PHQL
Retrocopy SKGYAFINFASFDALDAAIEAMNGQYLCNCPITMSYAFKKDSKGERHGSAAERLLAAQNPLSQADHPHQL

Parental  FADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAGT
          F.DAPPPPSAPNPVVSSLGSG.P.PGMPPPGSF.PPVPPPGALPPGIPPAMPPPP.PPGAGGH.P.SAG.
Retrocopy FTDAPPPPSAPNPVVSSLGSGFPLPGMPPPGSFAPPVPPPGALPPGIPPAMPPPPIPPGAGGHSP*SAGS

Parental  PGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLAHHGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMG
          PGAGH......HP..FPPGG.PHP.MSQ.QLAHH.PHGLGH.H.GPPGSGGQPPPRPPPGMPHPG.PPMG
Retrocopy PGAGH---SYPHP--FPPGGIPHPTMSQIQLAHHVPHGLGHHHVGPPGSGGQPPPRPPPGMPHPGLPPMG

Parental  MPPRGPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYG-YQRGPLPPPRPTPRPPVPPRGPLR
          M.PRGPPFGSPM.HPGPMP.HGM.GPPPLMPP.GY.G.P.PPPY..YQR.PLPPPRPTP.PPVPP...L.
Retrocopy MLPRGPPFGSPMDHPGPMPLHGMHGPPPLMPPCGYPGHPCPPPYA<YQRRPLPPPRPTPWPPVPPHDLLW

Parental  GPLPQ
          GPLPQ
Retrocopy GPLPQ

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_2804 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,