RetrogeneDB ID: retro_trub_9

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_399:66454..67597(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000005318
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: b4galt6 (1 of 2)
• Ensembl ID: ENSTRUG00000005726
• Aliases: None
• Description: UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6 [Source:ZFIN;Acc:ZDB-GENE-040426-789]

Sequence

>retro_trub_9
ATGGTTTACGTGAGGCGGCTGTTGGGAATCTCTAAACGAACTTTTCTGGCCTTGATATTCTTCCTAATCTCCAGCGCGTG
TCTCTACTTAATTTACGTGGCGCCTGGAATAGCCAACACATTGTTGTACGTGGTGCAAGCTCGAGGCATTGTGTTGAGGG
ACAACGTGAGGACCATTGAGCAAATGATGCGATTGTACATCAACAAGAACACAACATTTAACTGGACAAATGATCCTGCG
GGAAGGAGCGCCAGTGGATATCTGATGCAGCCAACCACCTACCTTCCAGAGAACTTCACCTACAGCCAGAACCTGCCCTG
CCCACAGCGTTTACCCTCCATGAAGGGCCACAGAGATGTAAACGTGGCAGAGATTTCCATGGAGGAGACAGAAGTCAGCT
TTACCAAATTCGCTGACATGGAGTTTGGAGGTCATTGGAAACCAAAGGACTGCATACCTCGCTGGAAAGTGGCCATTCTG
ATTCCGTTCAGAAACCGCCACGAGCATCTCCCCATCCTCTTGCAGCACCTCATTCCCATGCTGCTGCGGCAGAGATTGGA
GTTCGGCTTCTATGTCATTGAGCAGAGTGGGAGCCAGCCCTTCAACAGAGCCATGTTGTTCAATATCGGCTTTTTGGAGG
CCATGAAGGACTTGGACTGGGACTGTTTGATCTTCCATGACGTAGACCACATCCCAGAAAATGACCGAAACTACTACGGC
TGCGGGCAGATGCCACGCCATTTCTCTGCCAAACTGGACAAATACATGTATATTCTTCCATACAATGAATTCTTTGGAGG
TGTAAGCGGACTCACTGTGGAGCAGTTCCGCAGGATTAACGGCTTTCCCAATACATTCTGGGGCTGGGGGGGGGAGGATG
ATGACTTATGGAAGAGGGTTCACTACGCTGGTCTGAAAGTCACACGACCCGAAGGCGATATTGGCAAATACAAATCCATT
CCTCACCACCACAGAGGGGAGGTGCAGTTTCTTGGGAGGTATAAACTGCTGAGGTACTCCAAAGAGCGCCAATACTTGGA
TGGCCTTAACAATCTTCATTATAGCCCCCGTGTGTCCCTCAGAAGACTCTACAAAAACATCACGGTGGACCTGCACCCTG
AACTGGTCCCACTGAAGAGTAAC

Alignment

ORF - retro_trub_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.58 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVNWRRLPRMSNRSFLAFMFFFSMSTTCLYFIYVAPGIANTYFFMVQAQGIMLRDNVRTIGQMIRLYTNK
          MV..RRL...S.R.FLA..FF...S..CLY.IYVAPGIANT....VQA.GI.LRDNVRTI.QM.RLY.NK
Retrocopy MVYVRRLLGISKRTFLALIFFL-ISSACLYLIYVAPGIANTLLYVVQARGIVLRDNVRTIEQMMRLYINK

Parental  NSTLNGTDYPDGSNSSEYLVQPTTYLPENFTYAQNLPCPQRLPSMKGLIDVNMTEIPMEETELKFTKFFD
          N.T.N.T..P.G...S.YL.QPTTYLPENFTY.QNLPCPQRLPSMKG..DVN..EI.MEETE..FTKF.D
Retrocopy NTTFNWTNDPAGRSASGYLMQPTTYLPENFTYSQNLPCPQRLPSMKGHRDVNVAEISMEETEVSFTKFAD

Parental  IEFGGHWKPKDCVPHWKVAILIPFRNRHEHLPILFQHLLPMLQRQRLQFAFYVIEQSGSQPFNRAMLFNV
          .EFGGHWKPKDC.P.WKVAILIPFRNRHEHLPIL.QHL.PML.RQRL.F.FYVIEQSGSQPFNRAMLFN.
Retrocopy MEFGGHWKPKDCIPRWKVAILIPFRNRHEHLPILLQHLIPMLLRQRLEFGFYVIEQSGSQPFNRAMLFNI

Parental  GFLEAMKDLDWDCVIFHDVDHIPENDRNYYGCGQMPRHFAAKLDKYMYILPYNEFFGGVSGLTVEQFRKI
          GFLEAMKDLDWDC.IFHDVDHIPENDRNYYGCGQMPRHF.AKLDKYMYILPYNEFFGGVSGLTVEQFR.I
Retrocopy GFLEAMKDLDWDCLIFHDVDHIPENDRNYYGCGQMPRHFSAKLDKYMYILPYNEFFGGVSGLTVEQFRRI

Parental  NGFPNAFWGWGGEDDDLWNRVHYAGLNVTRPEGEIGKYKSIPHHHRGEVQFLGRYKLLRYSKERQHLDGL
          NGFPN.FWGWGGEDDDLW.RVHYAGL.VTRPEG.IGKYKSIPHHHRGEVQFLGRYKLLRYSKERQ.LDGL
Retrocopy NGFPNTFWGWGGEDDDLWKRVHYAGLKVTRPEGDIGKYKSIPHHHRGEVQFLGRYKLLRYSKERQYLDGL

Parental  NNLRYSPTISLSSLYKNISVDLHPELAPIE
          NNL.YSP..SL..LYKNI.VDLHPEL.P..
Retrocopy NNLHYSPRVSLRRLYKNITVDLHPELVPLK

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_9 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_9 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_9 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020816	1 retrocopy	retro_cjac_1251,
Monodelphis domestica	ENSMODG00000016301	1 retrocopy	retro_mdom_1782,
Ictidomys tridecemlineatus	ENSSTOG00000010911	1 retrocopy	retro_itri_1391,
Tetraodon nigroviridis	ENSTNIG00000010472	1 retrocopy	retro_tnig_6,
Takifugu rubripes	ENSTRUG00000005726	1 retrocopy	retro_trub_9 ,
Tursiops truncatus	ENSTTRG00000004300	1 retrocopy	retro_ttru_1533,