RetrogeneDB ID: retro_onil_19

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831331.1:995907..996966(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020871
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: cx34.5
• Ensembl ID: ENSONIG00000018317
• Aliases: None
• Description: connexin 34.5 [Source:ZFIN;Acc:ZDB-GENE-050224-2]

Sequence

>retro_onil_19
ATGGCAGACTGGAACTTGTTAGGGAAGCTGCTTGAAAGTGCTCAAGAGCACTCCACTGTAGTGGGCAAAGTCTGGTTGAC
GGTGCTGTTCATCTTCCGCATCCTGGTGCTGGGGGCTGCTGCTGAGAAGGTGTGGGGCGACGAGCAGTCCAGCTTCACGT
GTGACACCAAGCAGCCTGGTTGTCAGAACGTCTGCTATGACACGACCTTCCCCATTTCTCACATCCGCTTCTGGGTGATG
CAGATCATCTTTGTCTCCACGCCCACTCTCATTTATCTTGGTCATATCCTTCATTTGGTCCGTATGGAGGAGAAGGAGAA
GCAGAAACAAAAGGAGCTTGAAGACCAGCAGCAGGTACTCTGCCATAAGGACAAAAAGCCCTCAGTTAAAGACAAACAGG
GCCATGCACGTTTACAAGGTGCGCTGCTGCGGACCTATGTCTTCAACATTATTTTTAAGACCCTGTTTGAGGTAGCGTTT
ATTGTAGCTCAGTATTTTCTATATGGCTTTGAGCTCAAGGCCATGTACACCTGCGACCGCTGGCCTTGCCCAAACATGGT
GAACTGCTACATCTCCCGCCCCACTGAGAAGACAATCTTCATCCTTTTCATGCTGGCTGTAGCCTGCGTCTCACTGCTGC
TCAACCTGGTGGAAATGTACCATCTAGGTTTTACAAAGTGCCACCAGGGTCTTCGTTACAGGAGTTCAAAAGCCGCACGT
GAAGGTTCCAAAGCCCTAAGTGAGCCGGTCATGCCCTTTGTCCCAAACTATAACTATTTTGGAGGTCATTCTGCTGTGCC
TGAACCTTTCCCTACAGACTCAAAGTACGGCATGCCAGAACCAAACTCTGCTTACAGCCCCTACAACAGCAAGGTGGCCT
ACAAGCAGAACAGAGATAATATGGCTGTGGAGAGGAAAGGCAAAGCGGAAGAAAATGATATGAAGGGGAGGAAAATCTCC
AGTCCTGTCCTTGAGATGTCCATCGAAAATCAGCGCAGAAACAGCCAGTCAAGCAAGCACAGCAACTTTAAGAACAGGAT
GGATGACCTGAAGATCTAA

Alignment

ORF - retro_onil_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.64 %
• Parental protein coverage: 73.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGEWDLLGHLLDKVQSHSTVIGKVWLTVLFIFRIMVLQTGAEKVWGDEQSDFVCNTQQPGCENVCYDLAF
          M..W.LLG.LL...Q.HSTV.GKVWLTVLFIFRI.VL...AEKVWGDEQS.F.C.T.QPGC.NVCYD..F
Retrocopy MADWNLLGKLLESAQEHSTVVGKVWLTVLFIFRILVLGAAAEKVWGDEQSSFTCDTKQPGCQNVCYDTTF

Parental  PISHVRFWILQIIAIATPQLLYLGHVLHVIHVEKKMKERMKKQEELDDQTNLLLKRAYKVPKYTKSSGEI
          PISH.RFW..QII...TP.L.YLGH.LH....E.K.K....KQ.EL.DQ...L.....K.P......G..
Retrocopy PISHIRFWVMQIIFVSTPTLIYLGHILHLVRMEEKEKQ---KQKELEDQQQVLCHKD-KKPSVKDKQGHA

Parental  SIRGRLLRSYVLHLLAKIALEILFIVGQYLLYGFSLQTRYVCTRFPCPHKVDCFLSRPTEKSVIIWFMLV
          ...G.LLR.YV.....K...E..FIV.QY.LYGF.L...Y.C.R.PCP..V.C..SRPTEK...I.FML.
Retrocopy RLQGALLRTYVFNIIFKTLFEVAFIVAQYFLYGFELKAMYTCDRWPCPNMVNCYISRPTEKTIFILFMLA

Parental  AACVSLVLSLVELFYL
          .ACVSL.L.LVE...L
Retrocopy VACVSLLLNLVEMYHL

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_19 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_19 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000011933	2 retrocopies	retro_onil_22, retro_onil_29,
Oreochromis niloticus	ENSONIG00000013358	1 retrocopy	retro_onil_1,
Oreochromis niloticus	ENSONIG00000018317	1 retrocopy	retro_onil_19 ,