RetrogeneDB ID: retro_onil_3

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831198.1:1658092..1658983(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000021245
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: lrrc30
• Ensembl ID: ENSONIG00000009892
• Aliases: None
• Description: leucine rich repeat containing 30 [Source:ZFIN;Acc:ZDB-GENE-050506-25]

Sequence

>retro_onil_3
ATGGGTGGGAAGCAGTCCCGCAGTTTGTCCAGCAAGGAGTTGAGTGACATGAGCGTGAGCCAACGGAGACAGAGTGCAAT
TAGAGACGACCAGCCCAGCATGTCCTTGGCTGCTGGGAGGATCCGCAGACACACTAGACTGCATTTTGGTTACAGCACCC
TAAGTCTAGCCATGCGAGGACTAAATGAAACACCAACTGAACTATGGCAACTCCGAGACCTTCAGAAGCTAAACTTGTCA
ATGAACTGCCTGTGCTCTTTGCCCTCTTCCCTGGGTGCTCTTGACAATCTGGTGATTCTAAACTTGTGGGGGAACAACCT
GTCCCGCCTTCCACCTGAGATTGGCCTTCTAAAGAAACTGCGTGTGCTCTTCGCCTGTCGCAACCGCCTGAGTGAGGTAC
CAGAGGAGCTGGGCTCCTGTACCTGTCTGGAGGTGCTCAGTTTGGCCAATAATCAGATCACAGGCCTGCCAAGCAGCTTG
GCAGCCATGCGCAATCTGACGAAACTCAATCTCAGCCACAATCACATCGCTCACATTCCCACCTGCGTCTATAGCATGAA
GGGTCTGGTCTTCCTCCATCTCGCCTGCAACCGCCTGGAGACCATTGCGGACCAGATTCAGGACCTGGTTAATTTAAAAA
TCCTCATTGTGGAAGGAAATAGCATACACACATTGCCCAAAACTCTGTGCTTCCTGGAGTCTTTAGAACTCCTAAATGTT
GACTTCAATGATCTGCAAAGCGTACCAGTGGAAATGTACTTATTAAGTAAGCTGAGGCGGCTTGCGTGCCACCCGCTCGA
TAAAGGACTCCATATTGTGCATAACCCCCTTCTCAAACCTATCCAGGAGGTGCTACAAGGAGGACTCAGTGCTCTCTATA
ACTACCTCAAG

Alignment

ORF - retro_onil_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.5 %
• Parental protein coverage: 97.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKRRSEGREDSLT---SADRIRRFTIKQFGYNVLSLACRGLKEIPDELWELLELDKLNLSLNSLTVLPSQ
          ..R.S..R.D.......A.RIRR.T...FGY..LSLA.RGL.E.P.ELW.L..L.KLNLS.N.L..LPS.
Retrocopy QRRQSAIRDDQPSMSLAAGRIRRHTRLHFGYSTLSLAMRGLNETPTELWQLRDLQKLNLSMNCLCSLPSS

Parental  LALLSNLVVLNLWGNQLSSLPPEIGQLRKLRVLFAYRNRLKEVPEELGACTQLEVLSLANNQLSSLPASL
          L..L.NLV.LNLWGN.LS.LPPEIG.L.KLRVLFA.RNRL.EVPEELG.CT.LEVLSLANNQ...LP.SL
Retrocopy LGALDNLVILNLWGNNLSRLPPEIGLLKKLRVLFACRNRLSEVPEELGSCTCLEVLSLANNQITGLPSSL

Parental  SNLTQLRKLNLSHNLITHIPGCVYNMKALVFLHLACNRWGELENLAENIQALVELRILIVEGNSIHSLPK
          .....L.KLNLSHN.I.HIP.CVY.MK.LVFLHLACNR...LE..A..IQ.LV.L.ILIVEGNSIH.LPK
Retrocopy AAMRNLTKLNLSHNHIAHIPTCVYSMKGLVFLHLACNR---LETIADQIQDLVNLKILIVEGNSIHTLPK

Parental  ALCCLTRLELLNLNFNDIKDVPQEMHQLSRLEKLACHPLDKGLHIVHNPLLKPVKEVLEGGLSALFNYLR
          .LC.L..LELLN..FND...VP.EM..LS.L..LACHPLDKGLHIVHNPLLKP..EVL.GGLSAL.NYL.
Retrocopy TLCFLESLELLNVDFNDLQSVPVEMYLLSKLRRLACHPLDKGLHIVHNPLLKPIQEVLQGGLSALYNYLK

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_3 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_3 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000009892	1 retrocopy	retro_onil_3 ,
Tetraodon nigroviridis	ENSTNIG00000005041	1 retrocopy	retro_tnig_8,
Takifugu rubripes	ENSTRUG00000002387	1 retrocopy	retro_trub_22,
Xiphophorus maculatus	ENSXMAG00000002735	1 retrocopy	retro_xmac_4,