RetrogeneDB ID: retro_ogar_1714

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873562.1:6602932..6603849(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JMJD6
• Ensembl ID: ENSOGAG00000033219
• Aliases: None
• Description: jumonji domain containing 6 [Source:HGNC Symbol;Acc:19355]

Sequence

>retro_ogar_1714
ATGAAGCACAAGAATAAGAAGCTGTGCACAAGGCCAAGTGGAGTGTATAGCCAGTGCACAAGGACTCGCTGGACTGGACA
CAGTACAACTTCTAGCAGAGCCTCTCGCTGAGCCTGGCAGCATGGTAGACAACCTGAAAACAGCAAATGCTTTACAGCTA
CCTGTGGAAGAATTTGTGGAGTGACATAAAAGGCCAAACCAGCCCGTGGTTTTGCTGAATGCCTGAAGGTCTGCAAAGGA
GAACTAGACTTCAGAGCACCTAAAAAGGAAATACAGGAACCAGAAGTTCAAGTGTGGTGAGAATGACAATGGATGCTCAG
TGATGATGAAGATGAAATATTACATGGTGTACGTGGAGAGTATCGAGATGACAGTCCCCTTTGTGTCCTTGAAAGCACCT
ATGAGGAGCACCCCCAAAGAACAAAACTCTTGGAAGACCACAAGGTGCCCACATTTTGCTCTGATGACCTTTTCTAATAT
GCAGGGAAAAAGCACAGGTCCCTGACAGGCGCTTTGTAATGGTTCCACCGCACTCTGGAACTGGGATTCACACCAACTCT
CTGGGAAGCAGTACCTGGAACACCTTAGTTCAGGGCCCCAAGCTTATTCCCAAGAAGCACTTCCAGGCAGCTCATCTTCT
AACATGGGAAGAAGGATGGAACCAGCAGATGAAGCTATTACCTGGTTTAATGTGATTTATCCCTGGACACAGCCTCCAAC
CTGGCCACCTGAATTCAACCCCCTGGAAATCCTCCAAAAACCAGGAGAGACTGTCATTGTACTAGGACATGCTGTGGCAT
GTTGTCCATGACTGTCTTGACACTGCTATTGCTGCTACCCAGAACTTTGCCAACAGCACCAACTTCCCTGTTGTATGGCA
CAAGACAGTAAGAGGGAGACCTAAGTTATTAAGGAAA

Alignment

ORF - retro_ogar_1714 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.78 %
• Parental protein coverage: 75.12 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MNHKSKK-RIREAKRSARPELKDSLDWTRHNYYESFSLN-PAAVVDNVERADALQLSVEEFVERYERPYK
          M.HK.KK.....AK.S..P..KDSLDWT..N...S.SL..P...VDN...A.ALQL.VEEFVE...RP..
Retrocopy MKHKNKK<AVHKAKWSV*PVHKDSLDWTQYNF*QSLSLS<PGSMVDNLKTANALQLPVEEFVE*HKRPNQ

Parental  PVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCGEDNDGYSVKMKMKYYIEYMEST-RDDSPLYIFDSSY
          PVVLLNA....SA.E..T.E.LKRKYRNQKFKCGE...G.SV.MKMKYY..Y.ES..RDDSPL....S.Y
Retrocopy PVVLLNA*R--SAKEN*TSEHLKRKYRNQKFKCGENDNGCSVMMKMKYYMVYVESI<RDDSPLCVLESTY

Parental  GEHPKRRKLLEDYKVPKFFTDDLFQYAGEKRRP-PYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRW
          .EHP.R.KLLED.KVP.F..DDLF.YAG.K.R..P.R.FVM.PP.SGTGIH...LG.S.WN.LVQG.K..
Retrocopy EEHPQRTKLLEDHKVPTFCSDDLF*YAGKKHRS<PDRRFVMVPPHSGTGIHTNSLGSSTWNTLVQGPK--

Parental  CLFPTSTPRELIKVTREEGGNQQ-DEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGG-WWHV
          .L.P..........T.EEG.NQQ.DEAITWFNVIYP.TQ.PTWPPEF.PLEILQKPGETV.V.G...WHV
Retrocopy -LIPKKHFQAAHLLTWEEGWNQQ<DEAITWFNVIYPWTQPPTWPPEFNPLEILQKPGETVIVLGH>LWHV

Parental  VLN-LDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRK
          V...LDT.IA.TQNFA.STNFPVVWHKTVRGRPKL.RK
Retrocopy VHDCLDTAIAATQNFANSTNFPVVWHKTVRGRPKLLRK

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_1714 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019153	1 retrocopy	retro_btau_1374,
Otolemur garnettii	ENSOGAG00000033219	2 retrocopies	retro_ogar_1714 , retro_ogar_1715,