RetrogeneDB ID: retro_onil_11

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831403.1:550763..552272(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020404
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSONIG00000004218
• Aliases: None
• Description: None

Sequence

>retro_onil_11
CTGATCTCTTCAGGATTCCCTGCTGTCTATCAGCTGAGACCAAAGAAAGAGACATTTGGAACTTTGACAAGAATGACTGT
TGGTGAAAAAAATGTGAAGAAAACAAATAAAACCATCTTACTTGTGGGTGAATCAGGAACAGGAAAATCCACTTTGATCA
ATGCTCTGGTCAATTACACCATTGGAGTGAAGTGGGAGGATGAAGTCTGGTTTCAGATCTTAGAGGATGTAAGTACAAGT
CAGGCAGAAAGTCAGACTTCAGATGTGATCGTGTACGAGATCTTTGGTTTTGAAGATAAAACTCTGCCCTACTCTCTGAC
CATCATCGATACTCCTGGATATGGAGACACCAGGGGGATTGGATGTGATGAGATTGTCATTCAAAGATTATTTGACTTGT
TCCGATCAGACGATGGAGTTCGTGAAGTTCATGCAGTGGGTCTGGTGATGAAGGCGAGCGTTAATCGACTGAGTAACCGA
CTGTCATACATCTTTGATTCAGTGATGTCTCTGTTTGGAAAAGACATGGAGAAAAGCATTGTAGCTCTGATCACACACTC
AGATGGAAGACGTCCTAAAAATGCTTTTCAAGCTCTTGAAGCAGCAAAAATAAACTGTGCCAAAAATGAGAAGAACCAGC
CTGTTCACTTCCTGTTTAATAGCTGCCAGCATGAAGACCGAACAGAGGAAGAAGAATACCTGAAAATTGCTGGTCAAATA
TCAGAGAAAGGAATGAGAGATTTCACAGATTTTCTGGAAAAAACTTCACCTCAAAAACTTGACAAAACTGTGGATGTTCT
GAATGAACGAATCAGACTGACAGCCTGCATCCAAAACCTGCAAGACAGAATCAAACTCACCGAACTAAAGCAGACAGAAA
TCAGACAGATTCAAGAAGCTCTGAAAAAACATAAAGAAGGGATGAAAAAACATCAGAATTTCACTGTTGAACTTGATGAA
GTCTACAAAGATAAAAAACATATAAATGGTGGAATGTATTTTGTTTTTTATAGAGGAGCCGTCTGCTGTACAATCTGTGA
AGAGAACTGTCACTATCCTGGATGCACAATGGCCTGGTATGCTAAACACTGTGAGGTCATGAAAGATGGCTGCTGCACTG
TTTGCACTGGGAAGTGTCTTGCATTAGATCATGTGAAAGAAAACTGGATCTATGTGACAAAGACAAGAAAAATTCAGAGG
GCTATAGAAGATGTGAAACAGAAGTATGAAAAGCACAAGGCAGAAAGTCAAAACACACTGAGCTTGTTGCAAAATCTTGA
ACGTGAAATGAACCAACTGACAGCAGAGAAGTCACAGTTACTGGATGAGTCCTACCAACATCTTGTCAGACTGGAGCAGA
TCGCTCTGAAAGCTGATTCAGCGTCCACTATTCTCCACTTGGACTTCCTGATTGAGAAGATGGAGGAAGAAGGAAACACA
GAGAAGGTCCAGAAACTGGAGGAGATGAGAAGCAGAGTGGATGAAGGAACCAGAGTAGCTCTGCAGTAC

Alignment

ORF - retro_onil_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.05 %
• Parental protein coverage: 96.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LISSGPPAVYQLRPKKQKFGTLTRMTVGEKNPGKTNKTILLVGETGAGKSTLINALLNYTMGVKWEDGVW
          LISSG.PAVYQLRPKK..FGTLTRMTVGEKN..KTNKTILLVGE.G.GKSTLINAL.NYT.GVKWED.VW
Retrocopy LISSGFPAVYQLRPKKETFGTLTRMTVGEKNVKKTNKTILLVGESGTGKSTLINALVNYTIGVKWEDEVW

Parental  FQIIEEEDRSQTETQTSDVIMYEMFGFEDKTLPYSLTIIDTPGYGNTRGIGHDDIISHRLLDLFGSDDGV
          FQI.E....SQ.E.QTSDVI.YE.FGFEDKTLPYSLTIIDTPGYG.TRGIG.D.I...RL.DLF.SDDGV
Retrocopy FQILEDVSTSQAESQTSDVIVYEIFGFEDKTLPYSLTIIDTPGYGDTRGIGCDEIVIQRLFDLFRSDDGV

Parental  HEVHAAGLVMKASDNRLSDQLLYVFDSVMSLFGKIMEKNIVALITHSDGRRPKKLLQALEAANIKCAKNE
          .EVHA.GLVMKAS.NRLS..L.Y.FDSVMSLFGK.MEK.IVALITHSDGRRPK...QALEAA.I.CAKNE
Retrocopy REVHAVGLVMKASVNRLSNRLSYIFDSVMSLFGKDMEKSIVALITHSDGRRPKNAFQALEAAKINCAKNE

Parental  KNQPVYFLFNNSQYEDRTEENKFSKHLWELTQENMNQLTDFLGKSNPQKLMKTGEVLNERIRLKACIQNL
          KNQPV.FLFN..Q.EDRTEE....K.........M...TDFL.K..PQKL.KT..VLNERIRL.ACIQNL
Retrocopy KNQPVHFLFNSCQHEDRTEEEEYLKIAGQISEKGMRDFTDFLEKTSPQKLDKTVDVLNERIRLTACIQNL

Parental  KERIELSEMKQTEIRQMQEALKKHEELEEEMKRNKKFTVEVDEVYKEKETIDGGMRLLFFYEAAVCCTAC
          ..RI.L.E.KQTEIRQ.QEALKKH.E....MK....FTVE.DEVYK.K..I.GGM....FY..AVCCT.C
Retrocopy QDRIKLTELKQTEIRQIQEALKKHKE---GMKKHQNFTVELDEVYKDKKHINGGMYFV-FYRGAVCCTIC

Parental  EENCHYPGCTMAWKPAHCEVMKGGRCTVCTNKCPASDHVKEKWKYVTKTRRVTKTDEQMKKKYEKNVSEQ
          EENCHYPGCTMAW...HCEVMK.G.CTVCT.KC.A.DHVKE.W.YVTKTR......E..K.KYEK...E.
Retrocopy EENCHYPGCTMAWYAKHCEVMKDGCCTVCTGKCLALDHVKENWIYVTKTRKIQRAIEDVKQKYEKHKAE-

Parental  KEKECTLLENLEKEMKQLTAEKSQLLDESYQHVVRLEEIALKADSASTIVHLDFLIEKMKQKGDTEKVQK
          ......LL.NLE.EM.QLTAEKSQLLDESYQH.VRLE.IALKADSASTI.HLDFLIEKM...G.TEKVQK
Retrocopy SQNTLSLLQNLEREMNQLTAEKSQLLDESYQHLVRLEQIALKADSASTILHLDFLIEKMEEEGNTEKVQK

Parental  LEEMRSRVDKKNKKAAHW
          LEEMRSRVD.....A...
Retrocopy LEEMRSRVDEGTRVALQY

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_11 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_11 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	ENSONIG00000004218	1 retrocopy	retro_onil_11 ,