RetrogeneDB ID: retro_onil_9

Retrocopy location

• Organism: Tilapia (Oreochromis niloticus)
• Coordinates: GL831243.1:63531..64323(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSONIG00000020696
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: tnnt2a
• Ensembl ID: ENSONIG00000012310
• Aliases: None
• Description: troponin T2a, cardiac [Source:ZFIN;Acc:ZDB-GENE-000626-1]

Sequence

>retro_onil_9
ATGTCAGACACCGAGGAAATTGTGGAGGAATACGAGGAAGAGGTGGAAGAAGAGGTCGAGGAGGAAGAGGATGACAATGA
ACAGAGGCAAGCGGAGCACGAAGAAGAGACCAAACCTCGACCTAAAGCGACTTATGTGCCTAATATGGCTCCTCCAAAGA
TCCCAGATGGAGAAAGGGTGGATTTTGATGACCTGCATCGCAAGAGGCTGGAGAAAGATTACAATGACCTTCAGACACTG
ATTGAGCTGCATTTCACCAGCCGTCAGAAAGAGGAGGAAGAACTGATTGCGCTGCGTAACCGCATTGAATGCCGCCGCGC
TGACAGGGCCGAACAACAGCGTGTTCGTGCAGAGCAGGAGCGTGAGCGCCAGACGCGGGTTGCCGAGGAAAAAGCAAGGC
GTGAAGAGGAGGCAGCCAAACTGCGGGCTGAGGAGGAAGCCAAGAAGAAGATGGCTTTCTCCAACAAGTCATTCGGTGGC
TACTTGCAGAAGGTGGACCAGAAGAAGGGCAAGAAGCTAACAGCTCGTGAGGAGAAGAAGAAGGCCCTGATGGAGCGCAG
GAAACCACTCAACATCGACCACCTGAGCCAGGAGAAGTTGGTGGAGAAGGCACAGGAGCTCTGGCAGTGGCTCCACCAGC
TGCACGCCGAGAAGTTTGAGCTGGCAGAAAAGCTCAAGAGGCAGAAGTATGACATCCACGTGCTACGAAATCGCGTCAAC
GACCATCAGAGGTGGTCGAAAACATCCAAGACGTCCCGTGGGGCCAAGGGCAAGTCTGGCGCTTGGAAGTAA

Alignment

ORF - retro_onil_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.84 %
• Parental protein coverage: 92.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEDKPAAEEEANEEQDGEGEAEEGEEEEEAKPKFKPFIMPNLIPPKIPDGERVDFDDIHRKRMEKDLMEL
          EE.....EEE..EE.D...E....E.EEE.KP..K....PN..PPKIPDGERVDFDD.HRKR.EKD...L
Retrocopy EEYEEEVEEEVEEEED-DNEQRQAEHEEETKPRPKATYVPNMAPPKIPDGERVDFDDLHRKRLEKDYNDL

Parental  QTLIEVHFESRKKEEEELIQLKERIEKRRSERAEQQRIRSERDKERQKRLEDERIRKEEEEAKKRAEDDA
          QTLIE.HF.SR.KEEEELI.L..RIE.RR..RAEQQR.R.E...ERQ.R...E..R.EEE.AK.RAE..A
Retrocopy QTLIELHFTSRQKEEEELIALRNRIECRRADRAEQQRVRAEQERERQTRVAEEKARREEEAAKLRAEEEA

Parental  KKKKTLTSLHFGGYMQKLTDKRSGKRQTEREKKKKILNERRKSLDIENLSQERLKEKAKELWEWIQQLEA
          KKK.......FGGY.QK..D...GK..T.RE.KKK.L.ERRK.L.I..LSQE.L.EKA.ELW.W..QL.A
Retrocopy KKKMAFSNKSFGGYLQKV-DQKKGKKLTAREEKKKALMERRKPLNIDHLSQEKLVEKAQELWQWLHQLHA

Parental  EKFDLQYQFTRQKYEINVLRNRVSDHQKTSKRTK
          EKF.L.....RQKY.I.VLRNRV.DHQ..SK..K
Retrocopy EKFELAEKLKRQKYDIHVLRNRVNDHQRWSKTSK

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_9 retrocopy.

TSS

Oreochromis niloticus was not studied using FANTOM5 data.

Lab

retro_onil_9 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000020610	1 retrocopy	retro_drer_9,
Oreochromis niloticus	ENSONIG00000012310	1 retrocopy	retro_onil_9 ,
Oryzias latipes	ENSORLG00000006832	1 retrocopy	retro_olat_11,
Takifugu rubripes	ENSTRUG00000011858	1 retrocopy	retro_trub_31,