RetrogeneDB ID: retro_ogar_2954

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873689.1:1063469..1065083(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CUL2
• Ensembl ID: ENSOGAG00000005046
• Aliases: None
• Description: cullin 2 [Source:HGNC Symbol;Acc:2552]

Sequence

>retro_ogar_2954
TGGAGGAAGTCGATGCTTGAACCACTTCAGACCATTCTTAGAGGAACACTGCTCCGAGAAATAAAAAATGATCGTGGTGG
AGAACACTCAAACCAGAAAGCAATCCATGGGGTTACTGACTGCTGTGTTCATGTTGAACAGTATAAGAAAAAATTCCCCT
TCAAGTTTTATCAGGAAATATTTGAGTCCCCCTTTCTGACTGAAACAGGAGAGTATTATAAACAAGAAGCTTCAAATTTA
TTACAAGAATCAAACTGCTCACAGTATATGGGAAAGGTTCTAGGTAGATTAAGAGATGAAGAAATTCGATGTTGAAAATA
CTTAAATGCAAGTTCATAGACTAAAGTGATACATGAATGTCAACAATGAATGGTAGCAGGCCACTTAGAGTTCTTGCACG
CAGAATGTCACAATATCATTTCACAAGAGAAGAGAATGACATGGCAAATATGTATGTCTCACTCTGTGCTGTGTCCACTG
GTTTATCTCATAGGATTCAGGAGCTGCAAATCCATATCCATGATGAGGGCCTTAGAGCAACCAGTAACCTTACTCAGGAA
AATATGCCAACTGTATCTGTGGAATCAATTTTGGAAGTACACGGTAAATTTGTTCAACTTATTGACACTGTTTTGAATGG
TGATCAGCACTTTATGAGTGCACTGGATAAGGCCCTCACATCAGTTGTAAATTACAGAGAACCCAAGTCTGTTTGCAAAG
CACCTAAACTGCTTGCTTAGTACTGTGACAACTCACTAAAGGAATCAGCAAAAGGGATGACAGAGAATGAAGTGGAAGAC
AAACTCACAAGCTTCCTCACTGTTTTCAAATATATGGATGATGAAAATGTTTTTCAAAAGTTCTACACAAGAATGCTGGC
AAAACGTCTAATTCATGGGTTATCTGTGTCCATGGATTCCCAAGAAGCCATGATCCATAAATTAAAGCAAGCCCATGGTT
ATGAGTTACCAGCAAGCTACATCAGATGTATACAGATATGAGTGTCAGTGCTGAACTCAACAATAAGTTCAACAATTTTA
TCAAAAATCAAGACACAGAATGGATTTGGGAATTAGTTTTCAAATACATGCTCTACAGGCTGGTGCGTGGCCTCTAACTC
AGGCTCCTTCATCTACATTTGTGATTCCCCAGGAATTAGAGAAAAGTGTACAGATGTTTGAATTATTTTACAGCCAGCAT
TTCAGGGGAAGGAAACTGACCTGGTTACATTATCTGTGTACAGGTGAAGTTACAATGAACTATTTGGGCAAACCATATGT
AGCCATGGTCACAACATACCAAATGGCTGCCCTTCTTGCCTTTAACAACAGTGAAACTGTCAGCTGTAAAGAGCTTCAAG
ACAGCACTCAGTTGAATGAAAAGGAACTGACAGAAACAATCAAATCATTGCTTGATGTGAAAATGATTAACCACGATTCA
GAAAAGGAAGACATCGATGCAGAATCTTCATTTTCATTACATATGAACTTTAGCAGTAAAAGAACAAAATTAAAAATCAC
TACATCTATGCAGAAAGACACTCCACAGGAAATGGAGCAGACTAGAAGTGCTGTAGATGAGGACCAGAAAATGTATCTCC
AAGCTGCTATCGTG

Alignment

ORF - retro_ogar_2954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.19 %
• Parental protein coverage: 72.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WRKLMVEPLQTILIRMLLREIKNDRGGEDPNQKVIHGVIDSFVHVEQYKKKFPLKFYQEIFESPFLTETG
          WRK.M.EPLQTIL...LLREIKNDRGGE..NQK.IHGV.D..VHVEQYKKKFP.KFYQEIFESPFLTETG
Retrocopy WRKSMLEPLQTILRGTLLREIKNDRGGEHSNQKAIHGVTDCCVHVEQYKKKFPFKFYQEIFESPFLTETG

Parental  EYYKQEASNLLQESNCSQYMEKVLGRLKDEEIRCRKYLNASSYTKVIHECQQRMVADHLQFLHAECHNII
          EYYKQEASNLLQESNCSQYM.KVLGRL.DEEIRC.KYLNASS.TKVIHECQQ.MVA.HL.FLHAECHNII
Retrocopy EYYKQEASNLLQESNCSQYMGKVLGRLRDEEIRC*KYLNASS*TKVIHECQQ*MVAGHLEFLHAECHNII

Parental  RQEKK-NDMANMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLIN
          .QEK..NDMANMYV.L.AVSTGL.H.IQELQ.HIHDEGLRATSNLTQENMPT..VES.LEVHGKFVQLI.
Retrocopy SQEKR<NDMANMYVSLCAVSTGLSHRIQELQIHIHDEGLRATSNLTQENMPTVSVESILEVHGKFVQLID

Parental  TVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDKLTSFITVFKYI
          TVLNGDQHFMSALDKALTSVVNYREPKSVCKAP.LLA.YCDN.LK.SAKGMTENEVEDKLTSF.TVFKY.
Retrocopy TVLNGDQHFMSALDKALTSVVNYREPKSVCKAPKLLA*YCDNSLKESAKGMTENEVEDKLTSFLTVFKYM

Parental  DDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEF-TSKLHRMYTDMSVSADLNNKFNNFI
          DD..VFQKFY.RMLAKRLIHGLS.SMDS.EAMI.KLKQA.GYE..TSKLH.MYTDMSVSA.LNNKFNNFI
Retrocopy DDENVFQKFYTRMLAKRLIHGLSVSMDSQEAMIHKLKQAHGYEL<TSKLHQMYTDMSVSAELNNKFNNFI

Parental  KNQDTV-IDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMFELFYSQHFSGRKLTWLHYLCTGE
          KNQDT...DLGISFQI..LQAGAWPLTQAPSSTF.IPQELEKSVQMFELFYSQHF.GRKLTWLHYLCTGE
Retrocopy KNQDTE<MDLGISFQIHALQAGAWPLTQAPSSTFVIPQELEKSVQMFELFYSQHFRGRKLTWLHYLCTGE

Parental  VKMNYLGKPYVAMVTTYQMAVLLAFNNSEIVSYKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDID
          V.MNYLGKPYVAMVTTYQMA.LLAFNNSE.VS.KELQDSTQ.NEKELT.TIKSLLDVKMINHDSEKEDID
Retrocopy VTMNYLGKPYVAMVTTYQMAALLAFNNSETVSCKELQDSTQLNEKELTETIKSLLDVKMINHDSEKEDID

Parental  AESSFSLNMNFSSKRTKFKITTSMQKDTPQEMEQTRSAVDEDRKMYLQAAIV
          AESSFSL.MNFSSKRTK.KITTSMQKDTPQEMEQTRSAVDED.KMYLQAAIV
Retrocopy AESSFSLHMNFSSKRTKLKITTSMQKDTPQEMEQTRSAVDEDQKMYLQAAIV

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_2954 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000001282	2 retrocopies	retro_ogar_2069, retro_ogar_2642,
Otolemur garnettii	ENSOGAG00000005046	3 retrocopies	retro_ogar_1871, retro_ogar_2954 , retro_ogar_804,
Otolemur garnettii	ENSOGAG00000014715	1 retrocopy	retro_ogar_3491,