RetrogeneDB ID: retro_ogar_3423

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873827.1:80731..81986(-)
• 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_3423
ATGGAGTTCCAGCATAGGCCAGGGGGCAAGACTGGCAGTGGGGGCATGGCCTCCTCATGTGAGAAACTGGAACCGGCAGG
AACGCCTCCAGCAGCTGGCCCTGGAAGCCACCGACATCAACAAGGACCCATATTTTATGAAAAACCACCTGGGTTCATGT
GAATGCAATTTCTGCCTCATGCTTCACAACGAGGGAAGCTATCTCGTACATACCCAAGGAAAGAAGCTTCAAACCAACTT
GGCCCAGCGAGCAGCCAACAAGGCGAAGGAGGCCCCTTCCCCCAAGAAGGTCAAGGTAGAGGTGAAGAAGTTTGTGAAGA
TTGGCCGCCCAGGCTACAAAGTGACCAAGCAGAGGGACTCAGAGATGGGCCAGCAGAGCCTTCTCTTCCAGATCGACTAC
CCTGAGATTGCTGACGGCATCATGCCCTGCCACTGATTCATGTGTGCCTATGAGCAGAGGATAGAGCCCCCAGACCGGTG
CTGGCAATATTTGCTATTAGCTGCAAAGCCCTATGAGACCATCGCCTTCAAGGTACCTAGCAGAGAGATCAACAAGGCTG
AAGGCAAGTTTTGGACTCACTGGAATTGGGAAACCAAGCTGTTTTTCCTCCAGTTCCACTTTAAGATGGAGAAGCCCCAG
CTCCACCCAGCCTTCCTGCTGGTCCTCCTTGGGTGAAACGGCCTCTACCCTCAATGATGAATGGGTTGCCTCCTTGGCCT
CCATTGACTGAGTCTTTGCCACTACCCCTCCTTGGGGGCCTGGTCTGGCCCCCAATCCCTCCCAGGGCACTTGTACCCTC
AGGGCCCCCAAGACCTCCCCAACTGCCTCCACCAGCCCCTGGGGTCCACCCCCCAGCACTAGTGGTCCACTTCCCCCACG
TGTGGGGTCCACACTCCCCAGCCCCTGGGGTCCATTCCCTGGCACCAGTGGTCCACCGAACAGCATCTGGGGTTCACCGC
CCAGCTCCCAGTGTCCATCCCCAAGCTCCAGGGGTCCACCCTCCTCCATCAGCTGGGTTTCATCCTCAGGCCCCTGGAGT
ACATCCCGCAACTAATGCAGTTCACCCCCACACCCTAGGGGTCCACCCCTCAGCCCCAGGAATCCAACCTCAGCCCCTGG
GGGTCCACTCCTCAATTCCTTGTATCCAACTGCCAGCTCTTAGGGTCCAACCCTCAGCTCCTGGGGTCCACCCCCCAACT
CCCATGCCTCCAATGCTAAGGCCCCCACTCCCATCCGAAGGTCCCGGGAATATAC

Alignment

ORF - retro_ogar_3423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.13 %
• Parental protein coverage: 90.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDFQHRPGGKTGSGGVASSS-ESNRDRRERLRQLALETIDINKDPYFMKNHLGSYECKLCLTLHNNEGSY
          M.FQHRPGGKTGS.G...SS...N..R.ERL.QLALE..DINKDPYFMKNHLGS.EC..CL.LHN.EGSY
Retrocopy MEFQHRPGGKTGS-GGMASS>VRNWNRQERLQQLALEATDINKDPYFMKNHLGSCECNFCLMLHN-EGSY

Parental  LAHTQGKKHQTNLARRAAKEAKEAPAQPAPEKVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLLFQIDYP
          L.HTQGKK.QTNLA.RAA..AKEA...P.P.KVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLLFQIDYP
Retrocopy LVHTQGKKLQTNLAQRAANKAKEA---PSPKKVKVEVKKFVKIGRPGYKVTKQRDSEMGQQSLLFQIDYP

Parental  EIAEGIMPRHRFMSAYEQRIEPPDRRWQYLLMAAEPYETIAFKVPSREIDKAEGKFWTHWNRETKQFFLQ
          EIA.GIMP.H.FM.AYEQRIEPPDR.WQYLL.AA.PYETIAFKVPSREI.KAEGKFWTHWN.ETK.FFLQ
Retrocopy EIADGIMPCH*FMCAYEQRIEPPDRCWQYLLLAAKPYETIAFKVPSREINKAEGKFWTHWNWETKLFFLQ

Parental  FHFKMEKP-PAPPSLPAGPPGVKRPPPPLMNGLPPRPPLPESLPPPPPGGLPLPPMPPTGPAPSGPPGPP
          FHFKMEKP.PAPPSLPAGPP.VKRP.P..MNGLPP.PPL.ESLP.P..GGL..PP.PP....PSGPP.PP
Retrocopy FHFKMEKP<PAPPSLPAGPPWVKRPLPSMMNGLPPWPPLTESLPLPLLGGLVWPPIPPRALVPSGPPRPP

Parental  QLPPPAPGVHPPAPVVH-PPTSGVHPPAPGVHPPAPVVHPPTSGVHPPAPGVHPPAPVVHPPAS-GVHPP
          QLPPPAPGVHPPA.VVH.P...G.H.PAPGVH..APVVH...SGVH.PAP.VHP.AP.VHPP.S.G.HP.
Retrocopy QLPPPAPGVHPPALVVHFPHVWGPHSPAPGVHSLAPVVHRTASGVHRPAPSVHPQAPGVHPPPSAGFHPQ

Parental  APGVHPPAPGVHPPAPGVHPPPSAGVHPQAPGVHPSTTAVHPQAPGVHPQAPGIH-PQPPGVHPSAPGVH
          APGVHP....VHP...GVH.P...G..PQ..GVH.S.......A..V.P.APG.H.PQ.P......P..H
Retrocopy APGVHPATNAVHPHTLGVH-PSAPGIQPQPLGVHSSIPCIQLPALRVQPSAPGVH>PQLPCLQC*GPHSH

Parental  PPAPGVH
          P..PG..
Retrocopy PKVPGIY

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_3423 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,