RetrogeneDB ID: retro_tnig_12

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 7:6409047..6410112(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000011824
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: gja3
• Ensembl ID: ENSTNIG00000010339
• Aliases: None
• Description: gap junction protein, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-031217-3]

Sequence

>retro_tnig_12
ATGGGGGACTGGAACTTGTTGGGGAAGCTGCTGGAGAGTGCCCAGGAACACTCCACCGTTGTGGGCAAAGTCTGGCTGAC
AGTGCTGTTCATCTTCCGTATCCTGGTGCTGGGAACTGCCGCTGAGAAGGTGTGGGGAGATGAGCAGTCCGGCTTTACGT
GCGACACCAAGCAGCCCGGTTGTCAGAACGTTTGCTACGACAAGACCTTTCCCATTTCCCACATCCGCTTCTGGGTGATG
CAGATCATTTTCGTCTCCACGCCCACCCTCATCTATTTGGGCCACATCCTTCATCTGGTTCGCATGGAGGAAAAAGAGAA
ACAGAAAGAGAAGGAGCTGGCAGCCCAGAGTGAAAAACAGCAGCAGTTGCTTGGCAACAAGCCGAAAAAAGCCCCAATTA
AAGACAACCAGGGTCACGTGCGTTTGCAAGGCGCCCTGCTGCGAACTTACGTCTTCAACATCATCTTCAAGACCCTGTTT
GAAGTGGCCTTTATTGTAGCTCAGTACTTCCTCTATGGTTTCGAGCTCAAGCCGATGTACACCTGCGACCGCTGGCCTTG
CCCCAACATGGTGAACTGCTACATCTCTCGACCCACTGAGAAGACGGTCTTCATCCTCTTCATGCTGGCGGTGGCTTGCA
TCTCTCTGCTGCTCAACCTGGTGGAAATGTACCATCTGGGATTCACCAAGTGCCACCAGGGCCTTCGGTACAGGCGATCA
AAGACCAGAAAACAGTCTCCCAAGGCCCTCCACGAGCCCGTCATGCCCTTTGTTCCCAGTTACAACTACTACACCGGTCA
CCCTGCAGTGCCGGAGCCGTTTCCGACCGACTCCAAGTACAGCGTGACAGAGCCCGGCTCCGCTTACAGCCCCTACAGCA
ATAAGGTCGTCTACAAGCAGAACAGGGACAACATGGCTGTGGAGAGGAAGGGAAAACCCGAGGACGAGGTCGTGATGGAG
AGGAAACCCACCTGCCCTGCCTTTGAGGGGTCTGCTGACAGTCAGCGCAGAAACAGTCAGTCAAGCAAGCACAGCAAGAG
CAGACTGGATGACCTAAAGATCTAA

Alignment

ORF - retro_tnig_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.53 %
• Parental protein coverage: 67.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGDWSFLGRLLENAQEHSTVIGKVWLTVLFIFRILVLGAAAEEVWGDEQSDFTCNTQQPGCENVCYDEAF
          MGDW..LG.LLE.AQEHSTV.GKVWLTVLFIFRILVLG.AAE.VWGDEQS.FTC.T.QPGC.NVCYD..F
Retrocopy MGDWNLLGKLLESAQEHSTVVGKVWLTVLFIFRILVLGTAAEKVWGDEQSGFTCDTKQPGCQNVCYDKTF

Parental  PISHIRFWVLQIIFVSTPTLIYLGHVLHIVRMEEKRREREEELRKNGVSNGGGRGGGKKEKPPIRDEHGK
          PISHIRFWV.QIIFVSTPTLIYLGH.LH.VRMEEK....E.EL...........G...K.K.PI.D..G.
Retrocopy PISHIRFWVMQIIFVSTPTLIYLGHILHLVRMEEKEKQKEKELAAQSEKQQQLLGNKPK-KAPIKDNQGH

Parental  IRIRGALLRTYIFNIIFKTLFEVGFILGQYFLYGFHLRPLYKCGRWPCPNTVDCFISRPTEKTIFIIFML
          .R..GALLRTY.FNIIFKTLFEV.FI..QYFLYGF.L.P.Y.C.RWPCPN.V.C.ISRPTEKT.FI.FML
Retrocopy VRLQGALLRTYVFNIIFKTLFEVAFIVAQYFLYGFELKPMYTCDRWPCPNMVNCYISRPTEKTVFILFML

Parental  VVACISLALNLLEIYHLGWKKVKQGVTNEFVPDGEASPSVL
          .VACISL.LNL.E.YHLG..K..QG...........SP..L
Retrocopy AVACISLLLNLVEMYHLGFTKCHQGLRYRRSKTRKQSPKAL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_12 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000011933	2 retrocopies	retro_onil_22, retro_onil_29,
Tetraodon nigroviridis	ENSTNIG00000010339	1 retrocopy	retro_tnig_12 ,