RetrogeneDB ID: retro_onil_59

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831433.1:487521..488489(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000009972
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSONIG00000009973
• Aliases: None
• Description: None

Sequence

>retro_onil_59
GTTCCCCTGAAAGAAGAATATGAAGCAAAAAAAACACAACTTGGGATAACAGAGGCTAAAATTCAGCACATGATCCAAGA
GAGACAAAGAAAAGTCCAGGAGCTCAAACAATCCTTCGAGCTCAGCACAGAAGCTGCAGACAGAGAGACGGCAAATGGTG
TTCGGGTCTTCTCGGCTCTGATTAAGTCTCTGGAAAGAGCTCAGGCAGAGCTATTCGAGATGACTGAAAAAACCAGAAAA
GGACAGAGAAACAGATCAAAGTTTATATCAAAGAGCTGGAGCAGGAGGTCTTTGAGCTGACGAGGAGACGTGCTGAGATG
GAGGAAATCTCACGCTCTAAAGACCGTCTTCATTTTCTCCAGAGCTTCCCGTCCCTGAATGCTGCTCCACCCACCAAAGA
CTGGACAGATGTCAGCATCTGTCCAGCAATATACGAGGGAATCACAAGGACGGTTTTGGTGAAAGCTGTGGATGAGCTGA
CAGAGACTATCAAAAATGAGATGGAGATGATACGGGATGCTCAGTTCAACAACCTTCGACAGAATGCAGTGGATGTTACT
TTGGATCCTTATATGGCACATCCTGCTCTCATCCTGTCCAATGATAGGAAGCAAGTTCACTGTGGGGATGAATGGAAGAA
ACTGCCAGACAGATCAAAAAGATTTGAACCTGCAATTAATGTTTTAGGGACACAAGGCTTCTCCTGTGGAAGACTTTACT
ATGATGTCCAGGTTAAAGGAAAGACTGTGTGGATGTTAGGAGTGGCCAAAGGGTCGGTCAATAGGAAGGGAGAAATTAAA
CTAAACCCAGAGAACGGCTACTGGACTATATGTCTGAGGAACAGAAATGAGTACTTTGCACTTGCTGCCCATCCTGTCCC
TCTCTCTGTGAATGATGAGGTGAGAGTTTTTGTGGATTATGAGGAGGGTTTGGTTTCCTTTTATGATGTAAGTGCTGCTC
TAATCATC

Alignment

ORF - retro_onil_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.24 %
• Parental protein coverage: 75.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSLKELADSFAERLSLREYK--HMIQERQRKVQELKQSLKVSTEAADRETANGVRVFSALIQSLERAQAE
          V.LKE........L...E.K..HMIQERQRKVQELKQS...STEAADRETANGVRVFSALI.SLERAQAE
Retrocopy VPLKEEYEXXXXQLGITEAKIQHMIQERQRKVQELKQSFELSTEAADRETANGVRVFSALIKSLERAQAE

Parental  LIEMTEK-NQKRKEKQIKVYIKELEQEVFELTRRRAEMEEISRSKDRLRFLQSFLSLNAAPPTKDWTDVS
          L.EMTEK.NQKR.EKQIKVYIKELEQEVFELTRRRAEMEEISRSKDRL.FLQSF.SLNAAPPTKDWTDVS
Retrocopy LFEMTEK<NQKRTEKQIKVYIKELEQEVFELTRRRAEMEEISRSKDRLHFLQSFPSLNAAPPTKDWTDVS

Parental  IRPAIYEGITKTALVKAVDELTETIKNEMKMIRDAQFNNLRQNAVDVTLDPDTAHPALILSNDGKQVHCG
          I.PAIYEGIT.T.LVKAVDELTETIKNEM.MIRDAQFNNLRQNAVDVTLDP..AHPALILSND.KQVHCG
Retrocopy ICPAIYEGITRTVLVKAVDELTETIKNEMEMIRDAQFNNLRQNAVDVTLDPYMAHPALILSNDRKQVHCG

Parental  DERKKLPENPKRFEPAINVLGTQGFSCGRLYYDVQVKGKTGWTLGVAKGSVNRKGEIKLNPENGYWTICL
          DE.KKLP...KRFEPAINVLGTQGFSCGRLYYDVQVKGKT.W.LGVAKGSVNRKGEIKLNPENGYWTICL
Retrocopy DEWKKLPDRSKRFEPAINVLGTQGFSCGRLYYDVQVKGKTVWMLGVAKGSVNRKGEIKLNPENGYWTICL

Parental  RNRNEYFALAAHPVPLSVNDPPEKVRVFVDYEEGLVSFYDVNAAVLL
          RNRNEYFALAAHPVPLSVND....VRVFVDYEEGLVSFYDV.AA...
Retrocopy RNRNEYFALAAHPVPLSVND---EVRVFVDYEEGLVSFYDVSAALII

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_59 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_59 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oreochromis niloticus	ENSONIG00000009973	1 retrocopy	retro_onil_59 ,