RetrogeneDB ID: retro_ogar_2406

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873620.1:526375..527669(+)
• Located in intron of: ENSOGAG00000024767

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOGAG00000015920
• Aliases: None
• Description: None

Sequence

>retro_ogar_2406
CAGTTATCTGCTGCCAGCCAGAAGTTCAGGAAAAACACAGCCCATCTCTCTTGAGTCAGAAAAATATGGACCTAGCAAAG
TCAGGTATCAAGATACTTGTGCCTAAAAGCTCCATTAAGAACAGGACCTCAGTGGACGGCTTTGAGAATGAGAGCCCTGA
GAATCTGGACTCCATCAAGCAGGGTCAAAGAGACACAGTGGCACCCAAGGTGACATCAGAGAAGCCAGGTTGAGCTCTTT
TGGGCCCTGGTGCAGAGCGGACCAGGAAGGGGAGCAGGCCCCAGATACACCCACAAGTGCCTCAGGTACCTGGCCCTGTA
ACTACAGCCACGGCCACCGGCTTAGCCATGATGGGAAAGCTACATCTCCGTTCACGGATACATTAACAGCCAATGGAACA
ACCAACATACAGACATCTGTTACAGGAGTGACAGCTGGGAAAAGGAAATTTATTGATGACAGAAGAGACCAGCCTTTTGA
GAAGCGGTAGCATTTTAAGTGTGAGGCAAACAGAGAGTGCCTACGGATACAGAGATGCTGTCATCAGGACGCAGGATGGC
TTCATAGCTTCTTATCCACAAAATCATCAGAGAATAACTCTCTAAACCCAGAGGCAATGAAAGAAGTCCACAGTGCTCTG
ACCACAGCGACTGCTGGCGACAGCAAGGTGGTTCTGCTGAGTGCAGTTGGCAGTGGTTTTGTTGCAGTCTTCACTTTATG
TATTTTATGCAGTGTATAACAGATGACAGAAAAAGAGAAAGCACTAAAATGGTGGAAGCTCTAAGAAACTTCGTGAATAC
TTTCATTCAGTTTAAGAAGCCCATCATTGTAGCAGTAAATGGCCCAGCCATTGGTCTAGGAGCATCCATATTGCGTCTTT
GTGATGTGGTTTAGGCTAATCAAAAGGCTTGGCTTCAAAATCCTATACTTCCTTCGGACAGAGTCCAGATGGCTGTTCTA
CCGTTATGTTTCCCAAGATTACGGGAGGAGCATCTGCAAATGAAATGTTGCTCAGCGGGCGGAAGCTGACCACACAGGGG
GTGTGTGGCAAGGGCCTGGTCTCATAGGCATTCTGGCCCAGGACGTTCACCCAAGAAGTCATGGTTCCAATTAAGGAGCT
TGCCTCGTGTAATCCAGTGGTGCCTGAGGAAGCCAAAGCTCTTGTGTGCTATAACATGAAGATGGAGCTGGAATAGGCCA
ATGAGAGGGAGTGTGAAGTACTGAAGAAAATCTGGGGCTCTGCCCAGGGGATTGACTCCATGTTACAGTACTTCAGAGGA
AGATCGATGAGTTT

Alignment

ORF - retro_ogar_2406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.27 %
• Parental protein coverage: 79.93 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  QLFAASQKFRKNTA-PSLSSRKNMDLAKSGIKILVPKSPIKNRTSVDGFQNESPEKLDPVEQGQEDTVAP
          QL.AASQKFRKNTA.PSL.S.KNMDLAKSGIKILVPKS.IKNRTSVDGF.NESPE.LD...QGQ.DTVAP
Retrocopy QLSAASQKFRKNTA<PSLLSQKNMDLAKSGIKILVPKSSIKNRTSVDGFENESPENLDSIKQGQRDTVAP

Parental  EVTAEKPVGALLGPGAERARMGSRPRIHPLVPQVPGPVTAAMATGLAV-NGKGTSPFMDALTANGTTNIQ
          .VT.EKP..ALLGPGAER.R.GSRP.IHP.VPQVPGPVT.A.ATGLA...GK.TSPF.D.LTANGTTNIQ
Retrocopy KVTSEKPG*ALLGPGAERTRKGSRPQIHPQVPQVPGPVTTATATGLAM<DGKATSPFTDTLTANGTTNIQ

Parental  TSVTGVTAGKRKFIDDRRDQPFDKRLRF-SVRQTESAYRYRDIVVRKQDGFT-HILLSTKSSENNSLNPE
          TSVTGVTAGKRKFIDDRRDQPF.KR..F.SVRQTESAY.YRD.V.R.QDGF....L....S..N.SLNPE
Retrocopy TSVTGVTAGKRKFIDDRRDQPFEKR*HF>SVRQTESAYGYRDAVIRTQDGFI<SFLSTKSSENN-SLNPE

Parental  VMKEIQSALTTAAADDSKLVLLSAVGS-VFCCGLDFIYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKK
          .MKE..SALTTA.A.DSK.VLLSAVGS..FCC.L.F.YF....TDDRKRESTKM.EA.RNFVNTFIQFKK
Retrocopy AMKEVHSALTTATAGDSKVVLLSAVGS<WFCCSLHFMYFMQCITDDRKRESTKMVEALRNFVNTFIQFKK

Parental  PIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTP-YTTFGQSPDGCSTVMFPKIMGGASANEMLLSGRK
          PIIVAVNGPAIGLGASIL.LCDVV.AN.KAW.Q.P.YT.FGQSPDGCSTVMFPKI.GGASANEMLLSGRK
Retrocopy PIIVAVNGPAIGLGASILRLCDVV*ANQKAWLQNP<YTSFGQSPDGCSTVMFPKITGGASANEMLLSGRK

Parental  LTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPIVLEESKALVRCNMKMELEQANERECEVLKKIW
          LT.Q..CGKGLVS..FWP.TFTQEVMV.IKELASCNP.V.EE.KALV..NMKMELE.ANERECEVLKKIW
Retrocopy LTTQGVCGKGLVS*AFWPRTFTQEVMVPIKELASCNPVVPEEAKALVCYNMKMELE*ANERECEVLKKIW

Parental  GSAQGMDSMLKY-LQRKIDEF
          GSAQG.DSML.Y.LQRKIDEF
Retrocopy GSAQGIDSMLQY<LQRKIDEF

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_2406 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011787	1 retrocopy	retro_chof_525,
Callithrix jacchus	ENSCJAG00000021374	5 retrocopies	retro_cjac_2675, retro_cjac_3927, retro_cjac_4003, retro_cjac_4228, retro_cjac_4229,
Homo sapiens	ENSG00000153046	1 retrocopy	retro_hsap_4651,
Otolemur garnettii	ENSOGAG00000015920	2 retrocopies	retro_ogar_2406 , retro_ogar_3269,
Pan troglodytes	ENSPTRG00000017688	1 retrocopy	retro_ptro_3090,