RetrogeneDB ID: retro_onil_33

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831355.1:784725..785580(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020887
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: stom (2 of 2)
• Ensembl ID: ENSONIG00000013021
• Aliases: None
• Description: stomatin [Source:ZFIN;Acc:ZDB-GENE-980526-486]

Sequence

>retro_onil_33
ATGGCTGGCGACAACGAGGAAACCGCCCTGAAAGAAGCCAGGAGACGCGAGCGTCAGGTAACTTTGGAGAATGCAGACTC
GGACATCGGGTTTTGCGGCTGGCTGCTGGTCGGCCTCTCCCTCCTCCTCGTGCTGTTCACCCTGCCCTTATCTATCTGGA
TGTGCATCAAGATCGTGAAGGAGTACGAGAGGGCTATTATCTTCCGCCTGGGGCGCATTTTGCGCGGTGGAGCCAAAGGA
CCGGGTTTGTTCTTCATCGTGCCGTGCACCGACAGCTTCATTAACGTGGACATGCGCACCATCACCTTCGACATCCCACC
TCAAGAGGTTCTGACTAAAGACTCGGTGACAGTGAGCGTCGATGGCGTGGTCTACTATCGCGTCCAGAATGCTACCCTGG
CTGTGGCCAACATCACTAACGCGGATGCAGCCACGCGCCTGCTGGCCCAGACCACCCTGAGGAACGTGCTGGGCACCAAG
AACCTGGCCGAGATCCTGTCCGACCGCGAGGAGATCGCGCACAGCATGCAGTCCTCACTGGATGACGCCACGGATGACTG
GGGAATCAAGGTGGAGAGGGTGGAGATCAAAGATGTGAAGCTGCCCCTCCAGCTCCAGAGAGCCATGGCGGCTGAGGCAG
AGGCGAGCCGCGAGGCCCGAGCCAAGGTGATCGCCGCCGAGGGGGAGATGAACGCGTCGCGGGCGCTCAAGGAGGCCTCC
CTGGTGATTGCAGAGTCTCCGTCCGCCCTGCAGCTGCGCTACCTGCAGACCCTCAACACCATCGCTGCCGAGAAGAACTC
CACCATCATTTTCCCGCTGCCGCTGGAGATGATGCAGGGCTTCATCAAACACTGA

Alignment

ORF - retro_onil_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.08 %
• Parental protein coverage: 99.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADDKEDAEMKRARSRERQLALENPNTDIGFCGRILVGLSLILLLITLPISIWMCIVVVKEYQRAIIFRL
          MA.D.E....K.AR.RERQ..LEN...DIGFCG..LVGLSL.L.L.TLP.SIWMCI..VKEY.RAIIFRL
Retrocopy MAGDNEETALKEARRRERQVTLENADSDIGFCGWLLVGLSLLLVLFTLPLSIWMCIKIVKEYERAIIFRL

Parental  GRLLSGGAKGPGLFFVLPCTDNFINVDMRTVTFNIPPQKVLTRDSVAVCVDGVVYYRVQNPTLAVANVSN
          GR.L.GGAKGPGLFF..PCTD.FINVDMRT.TF.IPPQ.VLT.DSV.V.VDGVVYYRVQN.TLAVAN..N
Retrocopy GRILRGGAKGPGLFFIVPCTDSFINVDMRTITFDIPPQEVLTKDSVTVSVDGVVYYRVQNATLAVANITN

Parental  ADAATQLLAQTTMRNVLSSKNLAEILSDREDIAHFMQVTLDNATDDWGIEVERVEIKDVKLPPQLLRAMA
          ADAAT.LLAQTT.RNVL..KNLAEILSDRE.IAH.MQ..LD.ATDDWGI.VERVEIKDVKLP.QL.RAMA
Retrocopy ADAATRLLAQTTLRNVLGTKNLAEILSDREEIAHSMQSSLDDATDDWGIKVERVEIKDVKLPLQLQRAMA

Parental  SEAEATCEARAKVIAAEGEMSASRALKEASLVIAESPSALQLRYLQTLNTIAEEKNSTIIFALPLEILLK
          .EAEA..EARAKVIAAEGEM.ASRALKEASLVIAESPSALQLRYLQTLNTIA.EKNSTIIF.LPLE....
Retrocopy AEAEASREARAKVIAAEGEMNASRALKEASLVIAESPSALQLRYLQTLNTIAAEKNSTIIFPLPLEMMQG

Parental  FV
          F.
Retrocopy FI

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_33 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_33 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
Dasypus novemcinctus	ENSDNOG00000015723	1 retrocopy	retro_dnov_2496,
Nomascus leucogenys	ENSNLEG00000017145	1 retrocopy	retro_nleu_647,
Otolemur garnettii	ENSOGAG00000002879	2 retrocopies	retro_ogar_2886, retro_ogar_291,
Oreochromis niloticus	ENSONIG00000013021	1 retrocopy	retro_onil_33 ,