RetrogeneDB ID: retro_onil_62

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831518.1:28337..29075(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: brms1la
• Ensembl ID: ENSONIG00000019497
• Aliases: None
• Description: breast cancer metastasis-suppressor 1-like a [Source:ZFIN;Acc:ZDB-GENE-050913-49]

Sequence

>retro_onil_62
ATGCCATTGCACCGTGACCGGGAGAAAAAGGAGAGTACAGCTGAGGAGATGGAGGCAGAGGAACATGAGCAGGAGGCATC
AAGCTCAGAGGAGGAGGACTCTGACACTTCCTCTGTCTCTGAGGATGGAGACAGCTCAGAAATGGATGAGGAGGACTGTG
AGCGGAGAAGGATGGAGTGTCTGGATGAAATGTGCAACTTGGAGAAGCAATTCACTGATCTCAAAGACCAGTTGTATCGT
GAGCGTCTCAGTCAGGTTAACAGCAAGCTGGCAGAGGTGGAGGCTGGCCGGGCGGCAGAATATCTGGAGCCTCTGGCAGT
ACTGCTGGAGAACATGCAGGTCCGCACCAAGGTGGCAGGTATCTACAGAGAGTTGTGTTTGGAGTCTGTGAAGAACAAGT
ACGAATGTGAGATCCAGGCAGCATGCCAACACTGGGAGAGTGAGAAGTTGCTGCTGTTTGATACAGTGCAGAATGAGCTG
GAGGAGAAAATCCGAAGACTAGAGGAGGACAGGCACAGCATCGATATTACGTCAGAGCTGTGGAACGATGAGCTGTCAGG
AAGGAAGAAGAGGCGAGATGCTTTAAGTCCAGATAAGAAGAGGAGACGCCCATCGGTGGTGTCTGGTCCATATATTGTCT
ACATGCTACCAGATCTGGACATCCTAGAGGACTGGACCGCGATCAGGAAGGCCGTGGCTACGCTCGGGCCTCACAGAGGG
AGATCTGACTCTGAGAGC

Alignment

ORF - retro_onil_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPLHRDREKKESTAEEMEAEEHEQEASSSEEEDSDTSSVSEDGDSSEMDEEDCERRRMECLDEMCNLEKQ
          MPLHRDREKKESTAEEMEAEEHEQEASSSEEEDSDTSSVSEDGDSSEMDEEDCERRRMECLDEMCNLEKQ
Retrocopy MPLHRDREKKESTAEEMEAEEHEQEASSSEEEDSDTSSVSEDGDSSEMDEEDCERRRMECLDEMCNLEKQ

Parental  FTDLKDQLYRERLSQVNSKLAEVEAGRAAEYLEPLAVLLENMQVRTKVAGIYRELCLESVKNKYECEIQA
          FTDLKDQLYRERLSQVNSKLAEVEAGRAAEYLEPLAVLLENMQVRTKVAGIYRELCLESVKNKYECEIQA
Retrocopy FTDLKDQLYRERLSQVNSKLAEVEAGRAAEYLEPLAVLLENMQVRTKVAGIYRELCLESVKNKYECEIQA

Parental  ACQHWESEKLLLFDTVQNELEEKIRRLEEDRHSIDITSELWNDELSGRKKRRDALSPDKKRRRPSVVSGP
          ACQHWESEKLLLFDTVQNELEEKIRRLEEDRHSIDITSELWNDELSGRKKRRDALSPDKKRRRPSVVSGP
Retrocopy ACQHWESEKLLLFDTVQNELEEKIRRLEEDRHSIDITSELWNDELSGRKKRRDALSPDKKRRRPSVVSGP

Parental  YIVYMLPDLDILEDWTAIRKAVATLGPHRGISDSES
          YIVYMLPDLDILEDWTAIRKAVATLGPHRG.SDSES
Retrocopy YIVYMLPDLDILEDWTAIRKAVATLGPHRGRSDSES

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_62 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_62 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000016974	1 retrocopy	retro_ogar_2341,
Oreochromis niloticus	ENSONIG00000019497	1 retrocopy	retro_onil_62 ,
Ochotona princeps	ENSOPRG00000017354	1 retrocopy	retro_opri_1025,