RetrogeneDB ID: retro_ogar_557

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873523.1:41062821..41064259(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBAP1
• Ensembl ID: ENSOGAG00000015802
• Aliases: None
• Description: ubiquitin associated protein 1 [Source:HGNC Symbol;Acc:12461]

Sequence

>retro_ogar_557
ATGGCTTCTTGGAACTTGGGTGCAGATTTTCATGGGACTTTCTGTTACCTTGATGATGTCCCATTTAAGATAGGAGACAA
ATTCAAACCACTAAAGCTGGTCTACCTATTGGCTTTTCCTTTCCTGATGGTTTGCAGGTTGTCAGAGAAGTACAGTATGA
CTTCTCCTTGGAAAAGAAGACCATTGAGTGGGCTGAAGACACTAAGAAAACTCAAGAAGCTGAGCAGGAAGCAGAGCACA
AGATTGAGGAGGCAGAAGCTAAAGTGAATCCATAGAGTGGCCCAGAGGGCGATAGCAAAACGAGCTTTTCCAAGACTCAT
AGTAGAGCCACAATGCCACCTCCCTTTAACCCCATCCTTGCCAGCTTACAGCACAACAGCATCCTCATCCCAACTCGGTC
AGCAGTAATGCCAGGAAACAGAAGGTTCTCTGCCCACCCCACACAAAGGCAGATTTCAATCTTGCTGACTTGGAGTGTGA
AGAAGACCCATTTGATAGTCTGGAGTTAAAGACCACTGATGAGAAGGAAGAACAGAGAAACATTTTGGTAGGAACCACTG
AACCCATTATGGCTCAGTTATTGGACAATAACTTACCTAGAGGAGATTCTGGGTCTATGTTAGAGGATGAGGAGGTTCTG
GCATCCTTGGAGTGGGAGAACCTGGACTTGAAGCCTCTTCATAAACTCAATGGCTTTATAACCTTACCACAGTTGGGCAA
CTGTGAAAAGATGCTGCTGTCTTCCAAAGTGTCCCTCCCCTCATTCCTGCAGTAAGCAATATCAAATCCCTGTCCTTCCT
CAAACTTGACTCTGATGACAACAATCAGAAGACAGCCAAGCTAGCAAGCACTTCCCATAGCACCTCCTGCCTCTGCAGTG
GCACATTCCAGAATTCCCAAAAACCTTCCACACAAAGCAGTGCCAGTGAGCTCAATGGGCATCATACTCTTGGACTTTCA
GCTTTGAACTTGGGCAGTGGCACAGAGATGCCAACCCTGACATCCTCCTAGATGCCTTCCCACTCTTTATTGTCTGTGTG
CACCTCCAAATACAGGTCCCACAATTACCCCTCCTAATTTCTCAATGTCACAAGTACTCAACATACCCAGCTGTCCCCAG
GCCTATTCTGAACTACAGACACAATTTCCCAGTGAGCGGCAGTGTGTGGAGATAGTGGTCCATATGGGCTACTCATCTGA
GTGTGTCCTGAGAGCCATGAAGAAAAATGGAGAGAACATTGAACAGATTCTCGACTATTTCTTTGCACATAGACAGCTTT
GTGAGAAGGGCGTTGACCTTCTTTTAATGGAAGGGGCTCTGAAAATGCACTAGTGTTCAGAAGAGAAGATAATGGAGTTT
CTTCAGTTAATGAGCAAATTTAAGGAAATGGGCTTTGAACTGAAAGATGTTAAGAAGGTTTTGCTATTACACAATGAT

Alignment

ORF - retro_ogar_557 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.43 %
• Parental protein coverage: 96.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MASKKLGADFHGTFSYLDDVPFKIGDKFKTPAKV-GLPIGFSLPDCLQVVREVQYDFSLEKKTIEWAEDI
          MAS..LGADFHGTF.YLDDVPFKIGDKFK.P.K..GLPIGFS.PD.LQVVREVQYDFSLEKKTIEWAED.
Retrocopy MASWNLGADFHGTFCYLDDVPFKIGDKFK-PLKL<GLPIGFSFPDGLQVVREVQYDFSLEKKTIEWAEDT

Parental  KKIQEAEREAERKIEEAEAKVNSQSGPEGDSKMSITKTHSRATMPPPINPILASLQHNSILTPTR-VSSS
          KK.QEAE.EAE.KIEEAEAKVN..SGPEGDSK.S..KTHSRATMPPP.NPILASLQHNSIL.PTR.VSS.
Retrocopy KKTQEAEQEAEHKIEEAEAKVNP*SGPEGDSKTSFSKTHSRATMPPPFNPILASLQHNSILIPTR<VSSN

Parental  AMKQKVLSPPHTKADFNPADFECEEDPFDNLELKTIDEKEELRNILVGTTGPIVAQLLDNNLPRGGSGSM
          A.KQKVL.PPHTKADFN.AD.ECEEDPFD.LELKT.DEKEE.RNILVGTT.PI.AQLLDNNLPRG.SGSM
Retrocopy ARKQKVLCPPHTKADFNLADLECEEDPFDSLELKTTDEKEEQRNILVGTTEPIMAQLLDNNLPRGDSGSM

Parental  LEDEEVLASLERATLDFKPLHKPNGFITLPQLGNCEKMSLSSKVSLPP-IPAVSNIKSLSFPKLDSDDNS
          LEDEEVLASLE...LD.KPLHK.NGFITLPQLGNCEKM.LSSKVSLP..IPAVSNIKSLSF.KLDSDDN.
Retrocopy LEDEEVLASLEWENLDLKPLHKLNGFITLPQLGNCEKMLLSSKVSLPS<IPAVSNIKSLSFLKLDSDDNN

Parental  QKTAKLASTFHSTSCLRSGMFQNSQKPSTQSSVSELNGHHTLGLSALNLDSGTEMPTLMSSQMPSHSLLS
          QKTAKLAST.HSTSCL.SG.FQNSQKPSTQSS.SELNGHHTLGLSALNL.SGTEMPTL.SS.MPSHSLLS
Retrocopy QKTAKLASTSHSTSCLCSGTFQNSQKPSTQSSASELNGHHTLGLSALNLGSGTEMPTLTSS*MPSHSLLS

Parental  VCTEK-SSPPNTGPTVTPPNFSMSQVPNMPSCPQAYSELQTLSPSERQCVETVVNMGYSYECVLRAMKKK
          VCT.K...P..T.P............P..P...QAYSELQT..PSERQCVE.VV.MGYS.ECVLRAMKK.
Retrocopy VCTSK>TGPTITPPNFSMS--QVLNIPSCP---QAYSELQTQFPSERQCVEIVVHMGYSSECVLRAMKKN

Parental  GENIEQILDYLFAHGQLCEKGFDPLLVEEALEMHQCSEEKMMEFLQLMSKFKEMGFELKDIKEVLLLHNN
          GENIEQILDY.FAH.QLCEKG.D.LL.E.AL.MH.CSEEK.MEFLQLMSKFKEMGFELKD.K.VLLLHN.
Retrocopy GENIEQILDYFFAHRQLCEKGVDLLLMEGALKMH*CSEEKIMEFLQLMSKFKEMGFELKDVKKVLLLHND

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_557 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011672	1 retrocopy	retro_eeur_466,
Myotis lucifugus	ENSMLUG00000013063	1 retrocopy	retro_mluc_2305,
Otolemur garnettii	ENSOGAG00000015802	1 retrocopy	retro_ogar_557 ,
Ochotona princeps	ENSOPRG00000009100	3 retrocopies	retro_opri_355, retro_opri_477, retro_opri_680,
Ictidomys tridecemlineatus	ENSSTOG00000028294	1 retrocopy	retro_itri_1318,
Tarsius syrichta	ENSTSYG00000013035	2 retrocopies	retro_tsyr_1908, retro_tsyr_846,