RetrogeneDB ID: retro_onil_26

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831211.1:1439260..1441036(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020511
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KLHL25
• Ensembl ID: ENSONIG00000004042
• Aliases: None
• Description: None

Sequence

>retro_onil_26
ATGAAAATGTCTGTGTGCGTCCATGAGAACCGAAAATCGCGAGCCAGCACCGGCTCCATGAACATCTACCTTTTTCACAA
GTCCTCCTATGCTGACAGCGTACTCATGCACCTCAACTCGCTGCGGCAGCAAAGACTTTTCACCGACGTCTTGCTCCATG
CTGGCAGCCGCTCCTTTCCCTGCCACCGCGCCGTGTTGGCTGCCTGCAGTCGCTACTTTGAGGCCATGTTCAGCGGTGGC
CTGAGGGAAAGTCAGGCCAGTGAGGTTGACTTCCGTGACTCGATCCACCCGGAGGTTTTGGAGCTCCTGCTGGATTACGC
TTACTCATCACGGGTGGTCATCAATGAGGAGAATGCAGAGTCGCTGTTGGAGGCAGGGGACATGTTGGAGTTTCAGGACA
TCCGGGATGCCTGCGCAGAGTTCTTAGAGAGAAACCTTCACCCGTCCAACTGCCTTGGCATGCTTCTGTTGTCAGACGCC
CATCAGTGTATCAAGCTGTCAGAGCTCTCCTGGGGCATGTGCCTCAGCAACTTTCCTGCTATTTGCAAGACAGAGGACTT
CCTCCAACTGCCCAAAGATATGGTGGTGCAGCTTTTATCGCACGAGGAGCTAGAGACAGAAGACGAGAGACTGGTTTACG
AAGCTGCTCTTAACTGGATCAACTATGACTTGGAAAGGAGGCACTGCCATCTCCCGGAGCTCCTGAGAACGGTTCGCCTT
GCGCTGTTGCCTGCCATCTTTTTAATGGAGAATGTCTCTACCGAAGAGCTGATTAACTCCCAGGCCAAGAGCAAGGAGCT
GGTGGATGAAGCTATCCGCTGTAAGCTGAAAATCCTGCAGAACGATGGCGTTGTTAACAGCCCATGTGCTCGACCAAGAA
AAACCAGCCATGCCCTGTTTCTTCTGGGTGGCCAGACTTTCATGTGTGACAAGTTGTACCTCGTGGACCAGAAAGCCAAA
GAGATCATCCCAAAGGCTGACATCCCCAGTCCACGGAAGGAGTTCAGTGCCTGTGCAATTGGATGTAAGGTGTACATCAC
TGGTGGTAGAGGCTCAGAAAATGGCGTGTCCAAAGATGTTTGGGTCTATGACACTGTCCACGAGGAATGGTCAAAGGCGG
CACCCATGCTGATTGCCAGGTTCGGCCACGGGTCTGCAGAGTTGAAACACTGTCTCTACGTCGTAGGAGGTCACACCGCA
GCAACAGGCTGCCTTCCAGCTTCTCCATCAGTGTCTCTCAAACAGGTGGAGCAGTTTGACCCCGTGGCAAACAAGTGGAC
AATGGTAGCTCCTCTGAGAGAAGGTGTGAGCAACGCAGCTGTAGTTAGCGTCAAACTCAAACTCTTTGCTTTCGGAGGAA
CCAGCGTCACCCACGACAAGCTGCCCAAGGTGCAGTGCTACGATCCGCAGGAGAACCGATGGACCGTGCCTGCATCCTGC
CCTCAGCCATGGCGCTACACAGCCGCCGCTGTCCTGGGAAACCAGATCTTCGTCATGGGCGGAGACACAGAGTTCTCAGC
ATGCTCGGCATACAAGTTCAGCAGCGAGAGCTACCAGTGGACAAAAGTGGGTGATGTGACAGCCAAGAGAATGAGCTGCC
AGGCTGTGGCATCAGGGAACAAACTCTATGTGGTGGGTGGGTACTTTGGCACACAGCGGTGTAAAACTCTGGACTGCTAT
GACCCCACACTGGATGCATGGAACAGCATAACTACAGTGCCATACTCACTCATTCCTACTGCTTTCGTCAGCACCTGGAA
ACATCTACCTGCTTGA

Alignment

ORF - retro_onil_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVTVHENRKSRTSTGSMNISLFHKPSHPDSVLTHLNTMRKQCMFTDVTLWAGDRSFPCHRAVLAACSRY
          MSV.VHENRKSR.STGSMNI.LFHK.S..DSVL.HLN..R.Q..FTDV.L.AG.RSFPCHRAVLAACSRY
Retrocopy MSVCVHENRKSRASTGSMNIYLFHKSSYADSVLMHLNSLRQQRLFTDVLLHAGSRSFPCHRAVLAACSRY

Parental  FEAMFSGGLRESLDTDVNFRDSIHPEVLELLLDFAYSSRVIINEENAESLLEAGDMLQFHDIRDAAAEFL
          FEAMFSGGLRES....V.FRDSIHPEVLELLLD.AYSSRV.INEENAESLLEAGDML.F.DIRDA.AEFL
Retrocopy FEAMFSGGLRESQASEVDFRDSIHPEVLELLLDYAYSSRVVINEENAESLLEAGDMLEFQDIRDACAEFL

Parental  EKNLHASNCLGMMLLSDAHQCKRLYELSWRMCLVHYETVRESEDFYNLSKDQLLELILSDELEIEDEQVV
          E.NLH.SNCLGM.LLSDAHQC..L.ELSW.MCL.........EDF..L.KD....L....ELE.EDE..V
Retrocopy ERNLHPSNCLGMLLLSDAHQCIKLSELSWGMCLSNFPAICKTEDFLQLPKDMVVQLLSHEELETEDERLV

Parental  FNSVMRWVRYDLEGRRLHLPELLTGIRLALLPSECLLEAVACEELIMADKRSRSIVEEAMQCKKKILQND
          ......W..YDLE.R..HLPELL...RLALLP...L.E.V..EELI.....S...V.EA..CK.KILQND
Retrocopy YEAALNWINYDLERRHCHLPELLRTVRLALLPAIFLMENVSTEELINSQAKSKELVDEAIRCKLKILQND

Parental  GVVTSPCARPRKAGHTLLILGGQTFMCDKIYQVDHKAKEIIPKADLPSPRKEFSACAIGCKVYVTGGRGS
          GVV.SPCARPRK..H.L..LGGQTFMCDK.Y.VD.KAKEIIPKAD.PSPRKEFSACAIGCKVY.TGGRGS
Retrocopy GVVNSPCARPRKTSHALFLLGGQTFMCDKLYLVDQKAKEIIPKADIPSPRKEFSACAIGCKVYITGGRGS

Parental  ENGVSKDVWIYDTVHEEWSKGAPMLIARFGHGSAELENSLYVVGGHTAIAGVFPASPSVSLKQVERYDPL
          ENGVSKDVW.YDTVHEEWSK.APMLIARFGHGSAEL...LYVVGGHTA..G..PASPSVSLKQVE..DP.
Retrocopy ENGVSKDVWVYDTVHEEWSKAAPMLIARFGHGSAELKHCLYVVGGHTAATGCLPASPSVSLKQVEQFDPV

Parental  SNKWTMMAPLRDGVSNAAVVSAKVKLFVFGGTTIHRDKASKVQCYDPVGNRWNIAAECPQPWRYTAAAVL
          .NKWTM.APLR.GVSNAAVVS.K.KLF.FGGT....DK..KVQCYDP..NRW...A.CPQPWRYTAAAVL
Retrocopy ANKWTMVAPLREGVSNAAVVSVKLKLFAFGGTSVTHDKLPKVQCYDPQENRWTVPASCPQPWRYTAAAVL

Parental  GSQIFIMGGDTEFTAASAYRFDCEANQWTRVGDMTSKRMSCHAVASGNKLYVVGGYFGTQRCKTLDCYDP
          G.QIF.MGGDTEF.A.SAY.F..E..QWT.VGD.T.KRMSC.AVASGNKLYVVGGYFGTQRCKTLDCYDP
Retrocopy GNQIFVMGGDTEFSACSAYKFSSESYQWTKVGDVTAKRMSCQAVASGNKLYVVGGYFGTQRCKTLDCYDP

Parental  TSDSWNSITTVPYSLIPTAFVSTWKHLPA
          T.D.WNSITTVPYSLIPTAFVSTWKHLPA
Retrocopy TLDAWNSITTVPYSLIPTAFVSTWKHLPA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq

Oreochromis niloticus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_onil_26 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_26 was not experimentally validated.

Homology

Retrocopy orthology:

Oreochromis niloticus 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000004042	1 retrocopy	retro_onil_26 ,