RetrogeneDB ID: retro_onil_22

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831311.1:374821..376096(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020669
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: gja3
• Ensembl ID: ENSONIG00000011933
• Aliases: None
• Description: gap junction protein, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-031217-3]

Sequence

>retro_onil_22
ATGGGTGACTGGAGCTTTCTGGGTAATATTTTAGAGGAAGTCAACGAGCACTCTACGGTGATCGGCCGGGTGTGGCTCAC
AGTGCTCTTCATCTTTCGCATCCTCATCCTGGGCACAGCGGCAGAGTTTGTGTGGGGCGACGAGCAGTCTGATTATGTGT
GCAACACACAGCAGCCCGGATGTGAGAATGTGTGCTACGACGAGGCCTTCCCCATCTCCCACATTCGCCTGTGGGTGCTG
CAAATCATCTTTGTGTCCACGCCGTCTCTGGTGTACGTGGGCCACGCTGTCCACCATGTCCACATGGAGGAGAAACGCAA
AGAGCGGGAGGAGGCAGAACTTAGCCGGCAACAGGAGCTGAGTGAGGAGCGTCTCCCTCTGGCACCTGACCAGGGAAGTG
TCCGCACCACTAAGGAGACCAGCACGAAAGGCAGCAAGAAGTTCAGGCTGGAGGGCACCCTGTTGAGGACCTACATCTGC
CACATCATCTTCAAGACACTGTTTGAAGTGGGCTTTGTGGTGGGCCAGTACTTTCTGTATGGCTTCCGCATCTTGCCGTT
GTATAAATGCAGCCGCTGGCCCTGCCCCAACACGGTGGACTGCTTTGTGTCTCGCCCCACAGAGAAAACTGTCTTTATCA
TCTTCATGTTGGCTGTGGCCTGTGTCTCACTGTTCCTAAACTTTGTGGAGATCAGTCACTTGGGCTTGAAGAAGATTCGC
TTTGTCTTTCGAAAGCCAGCCCCAGCTCCGGGGCCATCCCAAGGCGAGGGGTCGGCCCCCCTGCCGCCACAAGGGAAGAG
CCTGCCCCCCTTGGCTGTTCCCTCTCTGCAGAGAGCAAAAGGTTACAGGCTGCTGGAGGAGGAGAAAGCTCCCCCCATGA
CTCACCTCTACCCACTGGCTGAGGTGGGCATGGAGGCTGGCAGAGGGGCTCCACCCTTCCAGGGGTTGGAGGAGAAAGTG
GAGGAAGTGCTGCCCATGGAGGACATCTCTAAGGTGTATGACGAGACTCTGCCCTCCTACGCCCAGACCACTGAGACAGG
AGGGGTGACATTACACGAGGAAGAGCCTGAGGAGGTGCAGCCGCCAGAGGTGGAAGCAGAGAGGGTGGATCTGGCTGCAG
AAGAGGACATCGAGGTAGAGGAGGCGGTGAACGGGGAGGGGGCAACTCCAGCAGAGGCAGGAACGGAAGCTGCAGAAACG
ATAGAAGACAACAGGCCGCTGAGCCGACTGAGCAAAGCCAGCAGCAGGGCCAGGTCAGACGATCTCACCGTATGA

Alignment

ORF - retro_onil_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.6 %
• Parental protein coverage: 50.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGDWSFLGRLLENAQEHSTVIGKVWLTVLFIFRILVLGAAAEEVWGDEQSDFTCNTQQPGCENVCYDEAF
          MGDWSFLG..LE...EHSTVIG.VWLTVLFIFRIL.LG.AAE.VWGDEQSD..CNTQQPGCENVCYDEAF
Retrocopy MGDWSFLGNILEEVNEHSTVIGRVWLTVLFIFRILILGTAAEFVWGDEQSDYVCNTQQPGCENVCYDEAF

Parental  PISHIRFWVLQIIFVSTPTLIYLGHVLHIVRMEEKRREREEELRKAGRHQDDHDPLYHNGVGDGGGKKEK
          PISHIR.WVLQIIFVSTP.L.Y.GH..H.V.MEEKR.ER..E.....R.Q.............G.....K
Retrocopy PISHIRLWVLQIIFVSTPSLVYVGHAVHHVHMEEKRKER--EEAELSRQQELSEERLPLAPDQGSVRTTK

Parental  PPIRDEHGKIRIRGALLRTYIFNIIFKTLFEVGFILGQYFLYGFQLRPLYKCGRWPCPNTVDCFISRPTE
          ........K.R..G.LLRTYI..IIFKTLFEVGF..GQYFLYGF...PLYKC.RWPCPNTVDCF.SRPTE
Retrocopy ETSTKGSKKFRLEGTLLRTYICHIIFKTLFEVGFVVGQYFLYGFRILPLYKCSRWPCPNTVDCFVSRPTE

Parental  KTIFIIFMLVVACVSLVLNLLEIYHLGWKKVK
          KT.FIIFML.VACVSL.LN..EI.HLG.KK..
Retrocopy KTVFIIFMLAVACVSLFLNFVEISHLGLKKIR

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_22 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_22 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 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,
Tetraodon nigroviridis	ENSTNIG00000010339	1 retrocopy	retro_tnig_12,