RetrogeneDB ID: retro_tnig_25

Retrocopy location

• Organism: Tetraodon (Tetraodon nigroviridis)
• Coordinates: 13:7660062..7661154(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: gcnt3
• Ensembl ID: ENSTNIG00000015814
• Aliases: None
• Description: glucosaminyl (N-acetyl) transferase 3, mucin type [Source:ZFIN;Acc:ZDB-GENE-110411-253]

Sequence

>retro_tnig_25
TGCCTGGCCATCATCGACGGGGACGTCGAGGGGAGGGAGAGGGACCTGGAACTTCTGCTGGCATCCAGGGCGAGACGGGA
TGTGTGGAACGAGACTTTCTTCATGAACGCGACGGCCGACTGCGCGTCCTACGTGGAGAGCCGAGGGTACATCACGGAGC
CCCTGAGCGAGGAGGAGAGGAACTTCCCCATCGCGTACTCCATGGTGATCCACGAGAAGATCGAGATGTTCGAGCGGCTC
CTGCGGGCCATCTACACCCCGCAGAACATCTACTGCGTCCACGTCGACCAGAAATCCCAGGATGAGTTCAAGGCGGCCGT
GGGGGCCATCGTGTCCTGCCTCCCCAACGTGTTCCTGGCCACCAAGATGGAGAGCGTGGTCTACGCGTCGTGGTCCCGCG
TCCAGGCGGACCTGAACTGCATGAGAGACCTGCTGGACTCCCAGGTCCAGTGGAAGTACCTGCTGAACACATGCGGGAGC
GACTTCCCCATCAAAACCAACCGGGAGATGGTGCAGACGCTGCAGACCCTGAGGGGCAGCAACAGCATGGAGTCGGAGAC
CACCAACGACTACAAGAAGGGCCGCTGGCAGTACCACCACCGGGTCACGGATCAGGTCGTCCGGACCGACGCGACCAAGG
GCCCCCCGCCCATAAACACCCCCATGTTCTCCGGGAACGCCTACTTCGTGGTGTCCAGGGCGTTTGTGCACCACGCGTTG
ACGGACGCGGAGGTGCAGGCGCTCCTGGAGTGGGAGAAGGACACCTTCAGCCCGGACGAGCACCTGTGGGCCACCCTGCA
GAGGATGCCCCGGGTCCCGGGGTCGGTGCCCCCCAACGACAAGTACGACACGTCGGACATGCTGGCCCTGGCGCGCGTGG
TCAAGTGGGGCTACTTAGCGGGGGACGTGGAGCAGGGGGCCCCGTACCGACCCTGCACCGGGGACTACAGGAGATCCGTG
TGCGTGTACGGAGCAGGGGACGTCCGGTGGCTCCTCGCACAAAGACACCTGTTGGCCAACAAGTTCGATCCTGAGATCGA
TGACGTCGCCATCAGGTGTCTGGAGTCGTATCTGCGCATGAAGGCTTTAAGT

Alignment

ORF - retro_tnig_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.04 %
• Parental protein coverage: 85.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CSAVLQGDQEEIEKAKILAITEAFQKSVQIPDEYYLSATENCRSFKIMRKYLQFPLSQEEKEFPLAYSMV
          C.A...GD.E..E....L.........V.........AT..C.S....R.Y...PLS.EE..FP.AYSMV
Retrocopy CLAIIDGDVEGRERDLELLLASRARRDVW-NETFFMNATADCASYVESRGYITEPLSEEERNFPIAYSMV

Parental  VHHKVQNFERLLRTIYAPQNIYCVHVDQKSTPSFRAAVTAIVSCFPNVFMVSQPVSVVYASWSRVQADIN
          .H.K...FERLLR.IY.PQNIYCVHVDQKS...F.AAV.AIVSC.PNVF......SVVYASWSRVQAD.N
Retrocopy IHEKIEMFERLLRAIYTPQNIYCVHVDQKSQDEFKAAVGAIVSCLPNVFLATKMESVVYASWSRVQADLN

Parental  CMADLYNSSINWKYFINVCGQDFPLKTNWEIVQMLRLLRGSNSMESEKMPEGKKWRVTKVHEVVDGAIQG
          CM.DL..S...WKY..N.CG.DFP.KTN.E.VQ.L..LRGSNSMESE.....KK.R....H.V.D.....
Retrocopy CMRDLLDSQVQWKYLLNTCGSDFPIKTNREMVQTLQTLRGSNSMESETTNDYKKGRWQYHHRVTDQVVR-

Parental  TEKHKEAPPFNLPILSGNAYIVVSRGYIRSVLEDKRIQVLIEWAKDTYSPDEFLWATIQRMPGVPGSTRP
          T...K..PP.N.P..SGNAY.VVSR......L.D...Q.L.EW.KDT.SPDE.LWAT.QRMP.VPGS..P
Retrocopy TDATKGPPPINTPMFSGNAYFVVSRAFVHHALTDAEVQALLEWEKDTFSPDEHLWATLQRMPRVPGSVPP

Parental  NAKFDMTDLNAIARLVKWQGHEGSDGSPDAVYAECQGRHVRGICVYGVGDLRWLLDQHHLFANKFDIEID
          N.K.D..D..A.AR.VKW.G....D....A.Y..C.G...R..CVYG.GD.RWLL.Q.HL.ANKFD.EID
Retrocopy NDKYDTSDMLALARVVKW-GYLAGDVEQGAPYRPCTGDYRRSVCVYGAGDVRWLLAQRHLLANKFDPEID

Parental  PFVIYCLEKYLRRKALA
          ...I.CLE.YLR.KAL.
Retrocopy DVAIRCLESYLRMKALS

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_25 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_tnig_25 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
Tetraodon nigroviridis	ENSTNIG00000015814	1 retrocopy	retro_tnig_25 ,