RetrogeneDB ID: retro_trub_29

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_190:474258..475458(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCTN1
• Ensembl ID: ENSTRUG00000003143
• Aliases: None
• Description: None

Sequence

>retro_trub_29
GAACGTGGTGTTCAGATGTCCTCCGCAGAAGGCTCGGCCTTCTCTGGATATCAGTATGGGGATATAATGGTGACCATAGG
AGAGAGGGGAGAGAGGGGGCGGCTCTGGCTGCCGAGCCCTGGTGTGAGCGCTCACTGTGTGGACACCAATCCTGCAGCTT
TCCTAGTGGAACAGAGGAGTCGGTGTTCCAGACATTTGGACCTGAGGAAAGACTGCAGCACTCTGCCAACCCTCAACATG
GCATCCTTCACCAGTATTCAAATGTTAGCTGGACGGATTGACAATGCCTCAGTGGTTCCCATGGAGGTAACTTCAGTCAT
CCTCCAGTCTGTGGAAGGGCCTCAGTCTGAGCTACAGGTGACTGCTGGAGAAAATCTCCGCCCCAGACTCCTGAATCAAA
CTCTCTGCAGTAATGTGGTGCTAAAGGCGGTCTATGTGGTTAAATATACCCCAGCTGGGAAAATTGTGAATGTGATGCTG
TCTCTGGTGATCGGGTTTATCCACGAAGCAGCGCTACCATTACTGCAGGAGTTTCAAATAGCATTTGTTCAGGATGAGGC
GACTGTCCACTACAGTGGGAATCCCGGATATGCGGTGGGACTTCCTCTTGTGTCTGGAACCATGACAGCAGATGGGATTA
CTAGAAGCATCAATCCCAGAGACACCATGTCTGTACTGTATAGTGCTGCAGACCAGGACTGTCTCAGGAACCCACATCAG
CGTTCACCCATCCTGTTCGGTGTTGACTTTGTGTCTGGCTGCACATTAAGATTGGAGGAAAATGTCAACTGTTCTCTTGT
CTCGCAAACTATGTTAAGAGTTCTGAGAGGATCAAATTATCCCCAGTATGTAGCTTCCTCTGGAAACTCCCCATTAGATG
CTCCCCAAGACTGGCTGCCAATCAGGAGCAACTTCCATCCTGGGGGAATACAGGGTTGCAGCATCCCTGTGTCATTTCAT
CTGGAAATGAAGTGGACCAAATATGGGTCTCTGGTGAACCCCCAGGCTCAGCTTGTGAGCATCCAGGAAATAATACAAAC
CGGCAACAGCAGTTTGGCCTTGTTATCCGGAGGCACCAACATCGTGCTAGTCAGCATCTCAGTGTCTTTTGTAGCTGTCA
GTGCTGGTGCTTCACCTGTTTACAGAGCAAAGCCCACTGTCGATGCAACACTACCTTCTAACTTCTTTTACCCTTTAGTC

Alignment

ORF - retro_trub_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.21 %
• Parental protein coverage: 76.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENGGQVSTSEDPAFSGYRYGDVLGTREESGERGRLWLPAPSVSARCVDTNPAAFLMDQSSRCTRPVVLES
          E.G.Q.S..E..AFSGY.YGD...T........RLWLP.P.VSA.CVDTNPAAFL..Q.SRC.R...L..
Retrocopy ERGVQMSSAEGSAFSGYQYGDIMVTIXXXXXXXRLWLPSPGVSAHCVDTNPAAFLVEQRSRCSRHLDLRK

Parental  DCSTLPTLNMDSYTSIQVLAVPFHTSMLEVVPMEISSIILQSVEGTQTELMMTAGKDLRPVLLNPSLCAN
          DCSTLPTLNM.S.TSIQ.LA.........VVPME..S.ILQSVEG.Q.EL..TAG..LRP.LLN..LC.N
Retrocopy DCSTLPTLNMASFTSIQMLAGRIDNA--SVVPMEVTSVILQSVEGPQSELQVTAGENLRPRLLNQTLCSN

Parental  VVLKVAYLMKYTPAGEIVNMALSLVIGFVHETALPLQQEFQIAFVQDEDEATVHYSGNPGYVIGLPLVSG
          VVLK..Y..KYTPAG.IVN..LSLVIGF.HE.ALPL.QEFQIAFVQDE..ATVHYSGNPGY..GLPLVSG
Retrocopy VVLKAVYVVKYTPAGKIVNVMLSLVIGFIHEAALPLLQEFQIAFVQDE--ATVHYSGNPGYAVGLPLVSG

Parental  TRTIVFTGIVRSLNPRDTLSVLSSSENQDCLQDPHQRSPILFGVDFVSGCSLRMEEVANCSLVSQTMLSV
          T.T....GI.RS.NPRDT.SVL.S...QDCL..PHQRSPILFGVDFVSGC.LR.EE..NCSLVSQTML.V
Retrocopy TMTA--DGITRSINPRDTMSVLYSAADQDCLRNPHQRSPILFGVDFVSGCTLRLEENVNCSLVSQTMLRV

Parental  LRGSNYPQYVASFGNSPLENPFDWLPVTSNFNPGETQSCSIPVSFQLEIQWTNYGSLVNPQAQLVSIKEV
          LRGSNYPQYVAS.GNSPL..P.DWLP..SNF.PG..Q.CSIPVSF.LE..WT.YGSLVNPQAQLVSI.E.
Retrocopy LRGSNYPQYVASSGNSPLDAPQDWLPIRSNFHPGGIQGCSIPVSFHLEMKWTKYGSLVNPQAQLVSIQEI

Parental  IQTNKSSLASLSGGSNILPITSSVSFVAVGAAASPGYRAMPTINAKLPADFFFPFV
          IQT..SSLA.LSGG.NI.....SVSFVAV.A.ASP.YRA.PT..A.LP..FF.P.V
Retrocopy IQTGNSSLALLSGGTNIVLVSISVSFVAVSAGASPVYRAKPTVDATLPSNFFYPLV

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_29 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_29 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	ENSTRUG00000003143	1 retrocopy	retro_trub_29 ,