RetrogeneDB ID: retro_tnig_6

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 21_random:2641888..2643037(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTNIG00000017581
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: b4galt6 (2 of 2)
• Ensembl ID: ENSTNIG00000010472
• Aliases: None
• Description: UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6 [Source:ZFIN;Acc:ZDB-GENE-040426-789]

Sequence

>retro_tnig_6
ATGGCCAACTGGAGGAGATTGACGCAAATGTCTCACCGATCATGTCTGGCCTTTGTATTATGCTTTTCCATGGCCACCAT
CTTTCTCTACTGCATTTACACAGCACCAAGTAGAGCAAACACATACTTCCTTATGGTGCAAGCTCAGGGCATCATGTTGA
GGAACAAAGTGAGAACCTTTGGTCAGATGATCCGATTGTACACCAAAAAGAACAGATCGGAAAACGGAATAGATAATACT
GATGAAAGTAGAACCAGTGAGTATCCGATGCAGCCAACCACTTACCTCCCAGAGAATTTTACCTATGCCCAGAACCTACC
CTGCCCACAGCGTTTACCTTCAATGAAGGGCCATATAGATACGAACATGACAGAGATTTCTATGGAGGACACAGAACTCA
GGTTCAACAAATTCTTTGATATCAAGTTTGGAGGTCACTGGAAACCAAAGGACTGCATACCTTACTGGAAGGTGGCCATC
CTGATTCCATTCAGAAACCGTCACGAACATCTACCTATCCTTTTCCAACACCTTATTCCCATGTTGCAGCGGCAGAGATT
GCAGTTTGCCTTCTACGTCATTGAGCAGAGTGGGAGCCAGCCCTTCAACAGGGCCATGCTCTTCAACATTGGGTTCACTG
AGGCCATGAAGGACTTAGACTGGAACTGCTTGATCTTCCATGACGTGGACCACATCCCAGAAGATGATCGGAACTACTAT
GGCTGTGAGCAGATGCCACGCCATTTTGCTGCCAAACTGGACAAATATATGTACATCCTGCCATATAATGAGTTCTTTGG
AGGTGTAAGTGGACTCACTGTGGAGCAGTTTCGCAAGATTAATGGCTTTCCTAATGCATTTTGGGGGTGGGGAGGAGAGG
ATGATGACTTGTGGAACAGAGTTCACTATGCTGGTCTGAACGTCACACGACCAGAAGGAGAGATTGGCAAGTACAAGTCT
ATTCCTCACCACCACAGAGGGGAGGTGCAGTTTCTTGGGAGGTATAAACTCTTAAGGTATTCCAAAGAACGGCAACATGT
GGACGGCCTTAACAATATTCATTATAACCCCGTTATTTCCCTCACTCCCCTCTACAAAAACATAAGCGTTGACCTGAAGC
CTGAACTGGCCCCCATTGAAGACTACTGA

Alignment

ORF - retro_tnig_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.08 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVNWRRLPRMSNRSFLAFIFFFSMSTTCLYFIYVAPGIANTYFFMVQAQGIMLRDNVRTIGQMIRLYTNK
          M.NWRRL..MS.RS.LAF...FSM.T..LY.IY.AP..ANTYF.MVQAQGIMLR..VRT.GQMIRLYT.K
Retrocopy MANWRRLTQMSHRSCLAFVLCFSMATIFLYCIYTAPSRANTYFLMVQAQGIMLRNKVRTFGQMIRLYTKK

Parental  NSTLNGTDYPDGSNSSEFLVQPTTYLPENFTYAQNLPCPQRLPSMKGLIDVNMTEIPMEETELRFSKFYG
          N...NG.D..D.S..SE...QPTTYLPENFTYAQNLPCPQRLPSMKG.ID.NMTEI.ME.TELRF.KF..
Retrocopy NRSENGIDNTDESRTSEYPMQPTTYLPENFTYAQNLPCPQRLPSMKGHIDTNMTEISMEDTELRFNKFFD

Parental  IEFGGHWKPKDCVPHWKVAILIPFRNRHEHLPILFQHLIPMLQRQRLQFAFYVIEQSGSQPFNRAMLFNV
          I.FGGHWKPKDC.P.WKVAILIPFRNRHEHLPILFQHLIPMLQRQRLQFAFYVIEQSGSQPFNRAMLFN.
Retrocopy IKFGGHWKPKDCIPYWKVAILIPFRNRHEHLPILFQHLIPMLQRQRLQFAFYVIEQSGSQPFNRAMLFNI

Parental  GFLEAMKDLKWDCLIFHDVDHIPENDRNYYGCGQMPRHFAAKLDKYMYILPYNEFFGGVSGLTVEQFRKI
          GF.EAMKDL.W.CLIFHDVDHIPE.DRNYYGC.QMPRHFAAKLDKYMYILPYNEFFGGVSGLTVEQFRKI
Retrocopy GFTEAMKDLDWNCLIFHDVDHIPEDDRNYYGCEQMPRHFAAKLDKYMYILPYNEFFGGVSGLTVEQFRKI

Parental  NGFPNAFWGWGGEDDDLWNRVHYAGLNVTRPEGEIGKYKSIPHHHRGEVQFLGRYKLLRYSKERQHLDGL
          NGFPNAFWGWGGEDDDLWNRVHYAGLNVTRPEGEIGKYKSIPHHHRGEVQFLGRYKLLRYSKERQH.DGL
Retrocopy NGFPNAFWGWGGEDDDLWNRVHYAGLNVTRPEGEIGKYKSIPHHHRGEVQFLGRYKLLRYSKERQHVDGL

Parental  NNLRYSPAVSLSSLYKNISVDLHPELAPIEDY
          NN..Y.P..SL..LYKNISVDL.PELAPIEDY
Retrocopy NNIHYNPVISLTPLYKNISVDLKPELAPIEDY

Legend:

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

Expression

RNA-Seq

Tetraodon nigroviridis was not studied using RNA-Seq expression data.

ChIP-Seq

Tetraodon nigroviridis was not studied using ChIP-Seq data.

EST

Tetraodon nigroviridis was not studied using EST data.

TSS

Tetraodon nigroviridis was not studied using FANTOM5 data.

Lab

retro_tnig_6 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_6 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,