RetrogeneDB ID: retro_onil_1

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831155.1:3203320..3204493(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000021343
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSONIG00000013358
• Aliases: None
• Description: Gap junction protein [Source:UniProtKB/TrEMBL;Acc:I3K6P7]

Sequence

>retro_onil_1
ATGAGTTGGAGCTTCCTCACACGCCTTTTGGATGAGATTTCCAATCACTCCACCTTTGTGGGCAAGATCTGGCTCACCCT
CCTCATTGTTTTTCGGATTGTGCTGACGGTTGTTGGAGGAGAGTCGATCTACTACGATGAACAGAGTAAATTTGTGTGTA
ACACGCAGCAACCTGGTTGCGAGAACGTATGCTATGACGCCTTTGCGCCATTGTCGCACATTCGCTTCTGGGTGTTTCAG
GTGATTATGATCACCACTCCCACCATCATGTACCTTGGGTTTGCTATGCACAAGATTGCTCGCATGGATGACGATGACTA
CAGGCCCCAGGGCAGGAAGAGGATGCCTATAGTGAGCCGTGGTGCTAACAGGGACTATGAGGAAGCAGAGGATAATGGGG
AGGAGGATCCTATGATCATTGAGGAAATTGAGCCAGAAAAGGAAAAGGAGGTTGCAGAAAAGCCCAAGAAAAAGCACGAT
GGGCGCCGTCGCATCAAGAGAGATGGCCTGATGAAGGTCTACGTGTTCCAGCTGCTATCCCGTGCCATCTTTGAGGCCGC
CTTCCTGTTTGGACAGTACATCCTTTATGGTCTGGAAGTGGCACCGTCGTACGTATGCACACGTTCCCCTTGCCCGCACA
CAGTGGATTGCTTTGTGTCACGCCCAACAGAAAAAAAGATCTTCCTGTTTATAATGTATGCCGTCAGCGCCTTGTGTCTC
CTCTTTACCCTGTTGGAGATCCTCCACCTTGGCATCAGTGGTATCCGCGACTGCTTTTGCACACCACGACCCCGGCACCC
CACCCCACGACACTCAGCTCTGGCCAGCCAGAGGTCCTCCATCTGCCGCCAGCCCTCTGCGCCTCCAGGCTATCACACTG
CTTTGAAGAAGGATCCATCTGGAAAACTGGGATTTCGAGATAACCTGGGAGACTCGGGTCGCGAGTCTTTCGGGGACGAG
GCATCATCTCGGGAGCTGGAGAGGCTGCGCAGGCACCTAAAACTGGCCCAGCAGCATCTGGATATGGCATACCAGAACGA
AGAGAACAGCCCGTCACGCAGCAGCAGCCCCGAATCTAACGGAACTGCAGTGGAGCAGAACAGGCTAAACTTTGCCCAGG
AAAAGCAGAGCAGTACCTGTGACAAAGGTGAGGCTTCTGTCTTTGTCTCTTGA

Alignment

ORF - retro_onil_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.84 %
• Parental protein coverage: 64.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSWSFLTRLLDEISNHSTFVGKVWLTVLIIFRIVLTAVGGETIYYDEQSKFVCNTQQPGCENVCYDAFAP
          MSWSFLTRLLDEISNHSTFVGK.WLT.LI.FRIVLT.VGGE.IYYDEQSKFVCNTQQPGCENVCYDAFAP
Retrocopy MSWSFLTRLLDEISNHSTFVGKIWLTLLIVFRIVLTVVGGESIYYDEQSKFVCNTQQPGCENVCYDAFAP

Parental  LSHVRFWIFQVIMITTPTIMYLGFAMHKIARMEETDFRPGPKRKKRMPIIKRGAARDYEEVEDNGEEDPM
          LSH.RFW.FQVIMITTPTIMYLGFAMHKIARM...D.RP.....KRMPI..RGA.RDYEE.EDNGEEDPM
Retrocopy LSHIRFWVFQVIMITTPTIMYLGFAMHKIARMDDDDYRP--QGRKRMPIVSRGANRDYEEAEDNGEEDPM

Parental  IAEEIEPEKTDKAEQSSEKKHDGRRRILRDGLMKVYVCQLLWRSAFEVAFLFGQYIMYGFEVIPSYVCTR
          I.EEIEPEK.........KKHDGRRRI.RDGLMKVYV.QLL.R..FE.AFLFGQYI.YG.EV.PSYVCTR
Retrocopy IIEEIEPEKEKEVAEKPKKKHDGRRRIKRDGLMKVYVFQLLSRAIFEAAFLFGQYILYGLEVAPSYVCTR

Parental  SPCPHTVDCFVSRPTEKTIFLLVMYVVSFLCLLLTILEIIHLGIGSIRDTF
          SPCPHTVDCFVSRPTEK.IFL..MY.VS.LCLL.T.LEI.HLGI..IRD.F
Retrocopy SPCPHTVDCFVSRPTEKKIFLFIMYAVSALCLLFTLLEILHLGISGIRDCF

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_1 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_1 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,