RetrogeneDB ID: retro_ogar_1641

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873558.1:10918748..10919942(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3A1
• Ensembl ID: ENSOGAG00000012931
• Aliases: None
• Description: splicing factor 3a, subunit 1, 120kDa [Source:HGNC Symbol;Acc:10765]

Sequence

>retro_ogar_1641
CCCTAAGCTCTCAAGTCCCTGCCTCCAGCCACTGGTCCAGATAAATATCTTATGTCCCCCATCACTGGAGAGAGGATCCT
TGCCAGCAAAATGCAGGAACACATGCGCATTAGGCTTCTCGACCCCCAGTGGCTGGAGCAGTAGGATCATTCCATTCATC
AGAAGCAGAGTGATGATGAGGTGTATGCACCAGGTCTAGATATTAAGATCAGCTTGAAGCAATTGGCTGAGTGGCATACT
GACATCTTTGGTGTAGAAGAAACTGCCATTGGGAAGAAGATTGGTGAGGAGGAGATCCAAAAGCCAAAGGAAAAGGTGAC
CTGGGATGGCCACTTGGGCAGCATGGCCTGGACTCAGCAGGCTGCCCAGGCAAACATCACTTTCCAGGAGCAGATTGAGG
CCATCCATAAGGCCAAGGGCCTGGTGCTAGAAGATGACACCAAAGAGAAGGTTGGTCCCAGTAAGCCCAGTGAAATCCCC
CAGCAGCCACTGCCTCCGTCTTTAGCCACCAACATCCTCAGCTCAGCCCCACCCATCTCAATGACCCAACCACCCACAAT
GCTGCCTCCTGACCATACTACAGTTGTCTCTGCAGTACCCATCATGCCCCACCCCCCAATGGCATCTCTGGTCCAGCTGC
CTCCTGGCTCAGTGACTGCCCCTATGCCACCCATTATCCACACACCCAAGATCAACATGGTGCTCATACCTCCCTTTGCC
CCTCCTATCATGGCACCCTGCCCACCCCCAATGATTGTGCCAACACCCTTTGTGCCTGTTCCACCCGTGGCAACTGTCCC
AGCTCTGGCCCCAATGGCCCCTATTCATCCCCCACCTCCCATGGAGGATGAGCCTGCCTCTAAGAAACTGAAGACAGAAG
ACAGCCTCATGCCTGAGAAAGAGTTCCTGCATAGGAACAAGGGTCCAGTGTCTATCAAAGTCCAGGTACCCAACATGCAG
GATAAGACAGAATGGAAACTGAAGGGATAGGTGCTGGTCTTCACCCTCCCGCTCACAGACCAGGTCTCTGTCATTAAGGA
GAAGATTCAGGAAGCCACAGGCATGCCTGCAGGGAAACAGAAACTGCAGTATGAGGGCATCTTCATCAAGGATCCCAACT
CGCTGGCTTACTACAATACAGCCAGTGGTGCGATCCTCCATCTGGCCCTCAGGGAGAGAGGCGGGAGGAAGAAG

Alignment

ORF - retro_ogar_1641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.71 %
• Parental protein coverage: 50.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKASKPLPPAPAPDEYLVSPITGEKIPASKMQEHMRIGLLDPRWLEQRDRSIREKQSDDEVYAPGLDIES
          P.A.K.LPPA..PD.YL.SPITGE.I.ASKMQEHMRI.LLDP.WLEQ.D.SI..KQSDDEVYAPGLDI..
Retrocopy P*ALKSLPPATGPDKYLMSPITGERILASKMQEHMRIRLLDPQWLEQ*DHSIHQKQSDDEVYAPGLDIKI

Parental  SLKQLAERRTDIFGVEETAIGKKIGEEEIQKPEEKVTWDGHSGSMARTQQAAQANITLQEQIEAIHKAKG
          SLKQLAE..TDIFGVEETAIGKKIGEEEIQKP.EKVTWDGH.GSMA.TQQAAQANIT.QEQIEAIHKAKG
Retrocopy SLKQLAEWHTDIFGVEETAIGKKIGEEEIQKPKEKVTWDGHLGSMAWTQQAAQANITFQEQIEAIHKAKG

Parental  LVPEDDTKEKIGPSKPNEIPQQPPPPSSATNIPSSAPPITSVPRPPTMPPPVRTTVVSAVPVMPRPPMAS
          LV.EDDTKEK.GPSKP.EIPQQP.PPS.ATNI.SSAPPI.S...PPTM.PP..TTVVSAVP.MP.PPMAS
Retrocopy LVLEDDTKEKVGPSKPSEIPQQPLPPSLATNILSSAPPI-SMTQPPTMLPPDHTTVVSAVPIMPHPPMAS

Parental  VVRLPPGSVIAPMPPIIHAPRINVVPMPPSAPPIMAPRPPPMIVPTAFVPAPPVAPVPAPAPMPPVHPPP
          .V.LPPGSV.APMPPIIH.P.IN.V..PP.APPIMAP.PPPMIVPT.FVP.PPVA.VPA.APM.P.HPPP
Retrocopy LVQLPPGSVTAPMPPIIHTPKINMVLIPPFAPPIMAPCPPPMIVPTPFVPVPPVATVPALAPMAPIHPPP

Parental  PMEDEPASKKLKTEDSLMPEEEFLRRNKGPVSIKVQVPNMQDKTEWKLNGQVLVFTLPLTDQVSVIKVKI
          PMEDEPASKKLKTEDSLMPE.EFL.RNKGPVSIKVQVPNMQDKTEWKL.G.VLVFTLPLTDQVSVIK.KI
Retrocopy PMEDEPASKKLKTEDSLMPEKEFLHRNKGPVSIKVQVPNMQDKTEWKLKG*VLVFTLPLTDQVSVIKEKI

Parental  HEATGMPAGKQKLQYEGIFIKDSNSLAYYNMANGAIIHLALKERGGRKK
          .EATGMPAGKQKLQYEGIFIKD.NSLAYYN.A.GAI.HLAL.ERGGRKK
Retrocopy QEATGMPAGKQKLQYEGIFIKDPNSLAYYNTASGAILHLALRERGGRKK

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_1641 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000009270	1 retrocopy	retro_mdom_1115,
Otolemur garnettii	ENSOGAG00000012931	1 retrocopy	retro_ogar_1641 ,