RetrogeneDB ID: retro_trub_31

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_21:1252959..1253625(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000014014
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TNNT2
• Ensembl ID: ENSTRUG00000011858
• Aliases: None
• Description: None

Sequence

>retro_trub_31
GCTGAAAAGGAAGAGGCTGAGAAGAAAGAGGAGCACGAGGAGTCCAGACCACGGCCGAAGGCCACATACGTACCAAATAT
GGCTCCTCCGAAGCTCCCCGATGGAGAGAAGGTGGATTTTGATGACCTGCATCGTAAGAGGCTGGAGAAGGACTACAACG
ACCTCCAGACGCTGATCGAGCTGCATTTCACCACCCGGCAGAAGGAGGAAGAGGAGCTGATCGCCTTACGAACGCGCATA
GAGCGTCGCCGGGCTGACCGGGCAGAGCAGCAGCGCATTCGCACCGAGCAGGAGCGCGAGCGCCAGACCCGCCTGGCCGG
GGAGAAGGCGAGGCGCGAAGAGGAGGCGGCGAAACTGCGCGCCGAGGAGGAGGCCAAGAAGAAGAAGATCTTCACCAATA
AGTCGTTCGGTGGCTACCTGCAGAAGGTGGATCAGAAGAAGGGCAAGAAGCTGACTGCCAGAGAGGAGAAGAAGAAGATC
CTGATGGATCGGCGGAAGCCCCTGAACATTGACCACCTGAACCAGGAGAAGCTGGAGGAGAAGGCGCAGGACCTGTGGCA
GTGGCTCCACCAGCTGCACGCCGAGAAGTTTGAGCTGGCGGAGAAGCTGAAGAGGCAGAAGTACGACATCTACGTGCTGC
GCAACCGAGTCAGCGACCACCAGAGG

Alignment

ORF - retro_trub_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.23 %
• Parental protein coverage: 83.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEEEEEEDPEHGEEAKPKFKPFIMPNLIPPKIPDGEKVDFDDIHRKRMEKDLMELQTLIEVHFESRKKEE
          AE.EE.E..E..EE..P..K....PN..PPK.PDGEKVDFDD.HRKR.EKD...LQTLIE.HF..R.KEE
Retrocopy AEKEEAEKKEEHEESRPRPKATYVPNMAPPKLPDGEKVDFDDLHRKRLEKDYNDLQTLIELHFTTRQKEE

Parental  EELIQLKERIENRRAERAEQQRIRSEREKERQKRLEDERTRKEEEEAKRRAEDDAKKKKTLTSLHFGGYM
          EELI.L..RIE.RRA.RAEQQRIR.E.E.ERQ.RL..E..R.EEE.AK.RAE..AKKKK..T...FGGY.
Retrocopy EELIALRTRIERRRADRAEQQRIRTEQERERQTRLAGEKARREEEAAKLRAEEEAKKKKIFTNKSFGGYL

Parental  QKLTEKRSGKRQTEREKKKKILSERRKSLDIDNLNQERLRDKAKELWEWMYQLEAEKFELQDQITKQKYE
          QK...K..GK..T.RE.KKKIL..RRK.L.ID.LNQE.L..KA..LW.W..QL.AEKFEL......QKY.
Retrocopy QKVDQKK-GKKLTAREEKKKILMDRRKPLNIDHLNQEKLEEKAQDLWQWLHQLHAEKFELAEKLKRQKYD

Parental  INVLRNRVSDHQK
          I.VLRNRVSDHQ.
Retrocopy IYVLRNRVSDHQR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_31 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_31 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_31 has 0 orthologous retrocopies within teleost group .

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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 ,