RetrogeneDB ID: retro_onil_29

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831347.1:823732..825157(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020652
• 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_29
ATGGGCGACTGGAGCTTTCTGGGGCGGCTGTTGGAGAACGCTCAGGAGCACTCAACGGTCATCGGCAAAGTCTGGCTGAC
TGTCCTCTTCATCTTCAGGATCCTGGTGCTGGGGGCTGCGGCCGAAGAGGTCTGGGGTGACGAGCAGTCCGACTTCACGT
GTAACACCCAGCAGCCCGGATGTGAGAACGTCTGCTATGACGAGGCCTTCCCCATCTCGCACATCCGCTTCTGGGTGCTG
CAGATCATCTTCGTGTCCACGCCAACCCTCATCTACCTGGGCCACGTGCTGCACATCGTCCGCATGGAGGAAAAGCGGAA
AGAAAAGGAGGAGGAGATGCGCAAGGCAAACAGGCTCCAAGAGGAGAAAGAACTCCTGTATAGAAATGGTGGTGATGTTG
GAGGAGGAGGAGGAGGAGGAGGCGGCAAAAAGGAGAAGCCGCCAATCAGGGACGAGCATGGCAAAATCCGTATCAGAGGC
GCGTTGCTGCGTACCTATGTGTTCAACATTATTTTCAAGACCCTGTTTGAAGTGGGATTCATTTTGGGCCAGTATTTTCT
CTATGGCTTCCAGCTGAGGCCCCTGTACAAGTGTGCACGTTGGCCCTGCCCCAACACCGTTGACTGCTTCATATCGAGGC
CCACTGAAAAGACTATTTTTATTATATTTATGCTTGTGGTGGCTTGCGTGTCTCTTTTGCTGAATTTGTTAGAGATCTAT
CACCTTGGATGGAAGAAAGTTAAACAGGGCATGACCAATGAGTATGCCCCTGACCGTGAGTCGCTGCGCCGCATCGACAT
TGCAGAGCCTGAGTGTTTGGCCTCGGCCTCCAGAACTGCCCCATCCAGCCCCAGCTACCCTCCCAACTACACAGATGTGA
CGGCGGGCAGCGGGGCGTTCCTGCCGCCCATGGGGCCAGCCGCCGTGCCCTCGGCCGCAGAGTTCAAGATGGACGACCTT
CAGCAGGAGGAGTCCCTCCAATCCTCCCCCTCTTCCCACTACTACATCAGCAACAACAACAACCACAGGCTGGCCACACA
GCAGAACTGGGCCAACCTGGCAACCGAGCAGCAGACTCGGGAGATGAAGGCCACCTCCCCTTCCTCTTCTTGTTCTGCCA
CCAGCAGCGACAATGAGCAGCACCAAAGCGTCAATGGTGCTCTGCTCCTACCCACCAGCAACACCACCAGTAACACCAAC
ATCACCAACGCGACTGCCAACGCTGCCTCCAGCGGCAGCAGCCCTGGCAACGCCTCCAACGCAGGCAGCTGGGATGGAGG
AAAGAGCGAGCAGGACGAAGGCCACGTCACCACCACAGTGGAGATGCACGAGCCTCCGGTAATGGTCAGCACAGACCCTC
GGCGGCTCAGTCGGGCCAGCAAGAGCAGCAGCATCAGGGCCAGGCCGAGTGATCTGGCTGTCTAA

Alignment

ORF - retro_onil_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.67 %
• Parental protein coverage: 61.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGDWSFLGRLLENAQEHSTVIGKVWLTVLFIFRILVLGAAAEEVWGDEQSDFTCNTQQPGCENVCYDEAF
          MGDWSFLGRLLENAQEHSTVIGKVWLTVLFIFRILVLGAAAEEVWGDEQSDFTCNTQQPGCENVCYDEAF
Retrocopy MGDWSFLGRLLENAQEHSTVIGKVWLTVLFIFRILVLGAAAEEVWGDEQSDFTCNTQQPGCENVCYDEAF

Parental  PISHIRFWVLQIIFVSTPTLIYLGHVLHIVRMEEKRREREEELRKAGRHQDDHDPLYHNG--VGDGGG--
          PISHIRFWVLQIIFVSTPTLIYLGHVLHIVRMEEKR.E.EEE.RKA.R.Q.....LY.NG..VG.GGG..
Retrocopy PISHIRFWVLQIIFVSTPTLIYLGHVLHIVRMEEKRKEKEEEMRKANRLQEEKELLYRNGGDVGGGGGGG

Parental  --KKEKPPIRDEHGKIRIRGALLRTYIFNIIFKTLFEVGFILGQYFLYGFQLRPLYKCGRWPCPNTVDCF
          ..KKEKPPIRDEHGKIRIRGALLRTY.FNIIFKTLFEVGFILGQYFLYGFQLRPLYKC.RWPCPNTVDCF
Retrocopy GGKKEKPPIRDEHGKIRIRGALLRTYVFNIIFKTLFEVGFILGQYFLYGFQLRPLYKCARWPCPNTVDCF

Parental  ISRPTEKTIFIIFMLVVACVSLVLNLLEIYHLGWKKVKRGVTNEFAPDSESLIMAEDEPTDAETSPEQTS
          ISRPTEKTIFIIFMLVVACVSL.LNLLEIYHLGWKKVK.G.TNE.APD.ESL............S...T.
Retrocopy ISRPTEKTIFIIFMLVVACVSLLLNLLEIYHLGWKKVKQGMTNEYAPDRESLRRIDIAEPECLASASRTA

Parental  PLVLDCLPAFGSVSVMGDGA
          P......P....V...G.GA
Retrocopy PSSPSYPPNYTDVTA-GSGA

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_29 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_29 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 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,