RetrogeneDB ID: retro_ogar_2588

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873636.1:6142108..6143642(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNL2
• Ensembl ID: ENSOGAG00000000469
• Aliases: None
• Description: cyclin L2 [Source:HGNC Symbol;Acc:20570]

Sequence

>retro_ogar_2588
GCAGCAGCAGTGGCGACCAGGGCTCTGGGCCTGCAGCCCCCAATGCAGCAGCTGGCACCCGGTGCTCAGGGAGCGCAGCC
CCGGGGTCTCAGGGAGAGTTGATTCAGAACAGGCTGTACTCCGCGGTGCTGATCACCTTGGAGAACTGCCTGCTGCCTGA
TGATGAGCTCCGCTTCACCCTGTCTATGTCGAGCAGCCTGCACACAAACACTGAGATCCACCTCTGAGTAATGGGCTGCA
AGCTCATCCAGGCAGCTGGCATCCTGCTCCATCTGCCGCAGGTGGCCATGGCTACCGGGTAGGTGCTGTTCCAGGGTTCT
TTTATGCCAAGTCCTTTGTGAAGTATTCCATGGAGCATGTGTCAATGGCCTGTGTTCACCGGGCTTCCAAAATAGAAGCA
GCTCCATAGACACGTAAGAGATGTTATCAATGTGTTCATAGACTTCAACAACTCAGAGAGAAAAAAGAAACCTCTGCCTT
TACTACTGGATCAAGATTATGTTAACTTAAACAACCAAATTATAAAAGTAGAAAGAAGAGTTCTCAAAGAGCTGGGTTTC
TGTGTCCACGTTAAACATCCTTATAAGAGAATCATTATGTACCTTCAGGTGTTAGAATGTGAGCATAACCAACAGCTGGT
CCAGACGTCATGGAATTACACGAATGACAGCTTTCACACTGATGTTTTCGTGTAGTTCCAGCCTGACAGCATTGCCTGTA
TCTGGATCTATCTCGCCGCCCGGACTCCGGAGATCCCTCTGCCCCAGTCATCCTCATTGGTTTCTTTTGTTTGCAGCAAC
TAAACAAGAAATTCAAGAAATCTGCTTAAAAATCCTACAGCTTTATACACGAAAAAAGGTTGATCTGAGTCACCTTTTTC
CATGGAAAAGAAGAAAGCACGCCATCCAGGAGGCAGACACAAGCGCAGGGCTTGCTCTCTGGAGGTGCACGGGCTGCAAA
CAGCACAGCAGGGTTCTCGCCTGCGCCCAAGCTGGAATCCTCCGAAGAAGTTAAGGGGAACAAAGCTTCTCAGCTCTCTG
TGAAGAGTACCAAGAGGAGAATTGAGGGTATGAAGAAAACCAAAGCTGACAGCCCCGTGAATGGCTTGCCAAAGGGGCAA
GAAATTCAAAGTCTCGAGCAGAGCTACTCGAGGTCCCCATCATGGTCTGCTTCTCCTAAGACGAAGAAAAGGGACAGTGG
CTCTGCATGTGGTGGGCTCCAAGTCACAGAGCTACTCTCGGAGCCAGAGCGATTCCCGGCCAAGACAGGCGCACCCCAGC
ACTCCCTACAAAGGCTCCGAGGCGAAGGGCTCCTGGAAGTCCAAACACTGCAGCTGTCCCACTTAGAAGCCACACGAGTC
TCAGAACCGGAGCTCATTCCGTTCTCGAAGCCGGTCACAGGAGCGGGCAGACAATGCTGGAAAATACAAGAAGCAAAGTC
ATTACTATAGAGATCAGCCAGGGAGCGTGCAGGGTCATCTGAGTGCACAGGCCATCCTCATGAGCGGGACCACCCTGGGC
ACAGCGGGCACCGG

Alignment

ORF - retro_ogar_2588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.85 %
• Parental protein coverage: 97.92 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  AAAAATGA-PGSAAPAAVAGAPGSGSAAPGLQGVLIGDRLYSGVLITLENCLLPDDKLRFTPSMSSGLDT
          AAA.AT.A..G.AAP.A.AG...SGSAAPG.QG.LI..RLYS.VLITLENCLLPDD.LRFT.SMSS.L.T
Retrocopy AAAVATRA<SGPAAPNAAAGTRCSGSAAPGSQGELIQNRLYSAVLITLENCLLPDDELRFTLSMSSSLHT

Parental  HTETDLRVVGCELIQAAGILLRLPQVAMATGQVLFQ-RFFYTKSFVKHSMEHVSMACVHLASKIEEAP-R
          .TE..L.V.GC.LIQAAGILL.LPQVAMATG.VLFQ..FFY.KSFVK.SMEHVSMACVH.ASKIE.AP.R
Retrocopy NTEIHL*VMGCKLIQAAGILLHLPQVAMATG*VLFQ<GFFYAKSFVKYSMEHVSMACVHRASKIEAAP>R

Parental  RIRDVINVF-HRLRQLRE-KKKLVPLLLDQDYVNLKNQIIKAERRVLKELGFCVHVKHPHKIIVMYLQVL
          ..RDVINVF.HRL.QLRE.KKK..PLLLDQDYVNL.NQIIK.ERRVLKELGFCVHVKHP.K.I.MYLQVL
Retrocopy HVRDVINVF<HRLQQLRE>KKKPLPLLLDQDYVNLNNQIIKVERRVLKELGFCVHVKHPYKRIIMYLQVL

Parental  ECERNQHLVQTSWNYMNDSLRTDVFVRFQPESIACACIYLAARTLEIPL-PSRPHWFLLFGATEEEIQEI
          ECE.NQ.LVQTSWNY.NDS..TDVFV.FQP.SIAC..IYLAART.EIPL.PS.PHWFLLF.AT..EIQEI
Retrocopy ECEHNQQLVQTSWNYTNDSFHTDVFV*FQPDSIACIWIYLAARTPEIPL>PSHPHWFLLFAATKQEIQEI

Parental  CLKILQLYTRKKVDLTHLEGEVEKRKHAIEEAKAQARGL-LSGGAQAADSTAGFSPAPKLVESPKEGKGN
          CLKILQLYTRKKVDL.HL......RKHAI.EA...A.GL.LSGGA.AA.STAGFSPAPKL.ES..E.KGN
Retrocopy CLKILQLYTRKKVDLSHL-FPWKRRKHAIQEADTSA-GL>LSGGARAANSTAGFSPAPKL-ESSEEVKGN

Parental  KASPLSVKSTKRRIEGMKKTKADSPVNGLPKGRESRSRSRSREQSYSRSPSRSASPKRRKSDSGSTSG-H
          KAS.LSVKSTKRRIEGMKKTKADSPVNGLPKG.E..S...S....YSRSPS.SASPK..K.DSGS..G..
Retrocopy KASQLSVKSTKRRIEGMKKTKADSPVNGLPKGQEIQSLEQS----YSRSPSWSASPKTKKRDSGSACG>G

Parental  SKSQSRSRSRSDSPPRQVHRSAPYKGSEVKGSRKSKDCKCPTQKPHKSQSRSSSRSRSRSRERADNAGKY
          SKSQS.SRS.SDS.PRQ.H.S.PYKGSE.KGS.KSK.C.CPT.KPH.SQ.RSS.RSRSRS.ERADNAGKY
Retrocopy SKSQSYSRSQSDSRPRQAHPSTPYKGSEAKGSWKSKHCSCPT*KPHESQNRSSFRSRSRSQERADNAGKY

Parental  KKKSHYYRDQP-RERARSYERTGHRYERDHPGHSRHR
          KK.SHYYRDQP.RERA.S.E.TGH..ERDHPGHS.HR
Retrocopy KKQSHYYRDQP<RERAGSSECTGHPHERDHPGHSGHR

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_2588 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000000469	1 retrocopy	retro_ogar_2588 ,
Otolemur garnettii	ENSOGAG00000001116	1 retrocopy	retro_ogar_2123,
Otolemur garnettii	ENSOGAG00000033279	1 retrocopy	retro_ogar_70,