RetrogeneDB ID: retro_trub_3

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_99:718888..719893(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000008847
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ccdc113 (2 of 2)
• Ensembl ID: ENSTRUG00000007278
• Aliases: None
• Description: coiled-coil domain containing 113 [Source:ZFIN;Acc:ZDB-GENE-041010-163]

Sequence

>retro_trub_3
ACATTCAGGAAAATGTCAGAGCCACAATTGGTATCATCAGGTGACTCAACAGACGATGAAAACCAAAGGATTCAGCTCCA
CCAACAAGTGGAAGAACTGAGAGGTTTTAATGAAGCACTCTTGGCAGAGAATGAGATGTTTGAGCAGTTCATCATCCACA
GTGATAAACAGAACCAGAAGTTCAGTGTAGACCCCCAACGGAACGATAAACTTAAAAAGGGTTCTAGCATCCGCTCAATA
TCCCAGTCTCGTGAGCTGACCATTGAGCAAAAACTTTATGTATCAGAGACGGCAATAAAAGAGGCACAAAAAGATCTGGA
GCAACTCAGAGAAAGAAATATGAAAACCTGGGATCACTATGTGTCCACCCTGGAAGAAGCAAAGTTGTGTCTTGAAGAAA
TCAGGAAAGGGAAGAAGGAATTTGAGCAAAAACTGCTCAGACGCGCGAATGAAAAAAGGCTGGAGATGAAAGAACCTGAG
AAGTTGCTCCTGTACATTGTCGACAAGTCCAAGACCACTAAAATTGAAATGTTGTCTATAAAGAACAGTGTATTAAAAGG
CCTCAAGAATAAGCTTAAGCATGATTTTCAACAGAAAAAAGAAAATCTTAAAATCTATTATGAAAAATCTGTCCTTTTCC
AAGGGTGGAGTAAGCAGAAAAGAGAAAAGCCCCTGGGGGAACTTCTAGGTGACTATGTAAAAACGCAGCATGTCATCACT
GTACATAAAGAGAAACAGAAGGGTGTGACAGCCGAACACACAAAGGTTTGCAAAAGGATTAAAAAGAGGGCGGAATTTCT
GGTAAAAACTGAGAATGACATTCAACAGGCGGAACAAGGACGTTTGAAGGCAGGAAACCTGAACCGACGCCTGCGCTCTC
AGATGGAAAATTATGAGGTCCCTGAGGTAAAGGAGTACTTAGAAGCCAGGAGGAGATACAAGAAGCTGCAGCAGGATATT
CGAATTTGGGAGAGGAAGGTCAAGATTGCTCAGATGATTTTATAG

Alignment

ORF - retro_trub_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.16 %
• Parental protein coverage: 51.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKDGRVSTACRRHQLTLEEKLHVSREEIAEAQKDLENLRETNEGTCDAYKASLKEAGLHLEEIRKAKNEF
          .K............LT.E.KL.VS...I.EAQKDLE.LRE.N..T.D.Y...L.EA.L.LEEIRK.K.EF
Retrocopy KKGSSIRSISQSRELTIEQKLYVSETAIKEAQKDLEQLRERNMKTWDHYVSTLEEAKLCLEEIRKGKKEF

Parental  EHKMQERMNDKRLEMKEPEKCLQYLEDKAKAAQVEILRLKNGALKVIENKLKHNFHQKREKGKTSYEE--
          E.K...R.N.KRLEMKEPEK.L.Y..DK.K....E.L..KN..LK...NKLKH.F.QK.E..K..YE...
Retrocopy EQKLLRRANEKRLEMKEPEKLLLYIVDKSKTTKIEMLSIKNSVLKGLKNKLKHDFQQKKENLKIYYEKSV

Parental  IFQDWGEHKSEKSLDELRANSLEVQRVLTVHK
          .FQ.W...K.EK.L.EL.......Q.V.TVHK
Retrocopy LFQGWSKQKREKPLGELLGDYVKTQHVITVHK

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_3 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_3 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_3 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Takifugu rubripes	ENSTRUG00000007278	1 retrocopy	retro_trub_3 ,