Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin beta-3 chain.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g5213 g5213.t2 isoform g5213.t2 7841357 7842017
chr_2 g5213 g5213.t2 exon g5213.t2.exon1 7841357 7842017
chr_2 g5213 g5213.t2 TTS g5213.t2 7841359 7841359
chr_2 g5213 g5213.t2 cds g5213.t2.CDS1 7841424 7842008
chr_2 g5213 g5213.t2 TSS g5213.t2 NA NA

Sequences

>g5213.t2 Gene=g5213 Length=661
GCTGTCAATATGGTTCCTTTCCCACGTCTTCATTTCTTCATGCCCGGTTTCGCGCCATTG
ACAGCTAAGAACAGTCAACAATATCGCGCTTTGACTGTTAATGAATTAACACAACAAATG
TTTGATGCCAAAAATATGATGACAGCTTGTGATCCAAGACACGGTCGTTATTTGACTGTT
GCTGCAATTTTCCGTGGTCAAATGTCAATGAAAGAAGTTGATGAACAAATGTTGGGTGTG
CAGAATAAAAACAGCAGCTATTTTGTCGAGTGGATTCCAAACAATGTAAAAGTTGCTGTT
TGTGATATTCCACCGAGAGGTCTTCGTATGGCAGCAACATTCATTGGAAACACAACAGCA
ATTCAAGAAATTTTCAAGCGAATTTCTGAGCAATTTACAGCAATGTTCCGTCGTAAAGCT
TTCTTGCATTGGTACACAGGTGAAGGAATGGATGAAATGGAATTCACTGAAGCTGAGAGC
AACATGAATGACTTGGTATCAGAATATCAACAATATCAAGAAGCTACAGCAGAAGATGAT
GTTGAATATGATGATCAGGGTGAAGTCATCGAAGAAGAAGGACCACAAGAATAAAGAAAA
TTATTTTGTATCAAAAAAATATTATTGTAATAAAGTTAAGACAATTTAGTCACTTTCATA
A

>g5213.t2 Gene=g5213 Length=194
MVPFPRLHFFMPGFAPLTAKNSQQYRALTVNELTQQMFDAKNMMTACDPRHGRYLTVAAI
FRGQMSMKEVDEQMLGVQNKNSSYFVEWIPNNVKVAVCDIPPRGLRMAATFIGNTTAIQE
IFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQEATAEDDVEY
DDQGEVIEEEGPQE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g5213.t2 Coils Coil Coil 152 172 -
12 g5213.t2 Gene3D G3DSA:3.30.1330.20 - 4 117 4.5E-56
11 g5213.t2 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 118 189 4.0E-35
15 g5213.t2 MobiDBLite mobidb-lite consensus disorder prediction 173 194 -
2 g5213.t2 PANTHER PTHR11588:SF279 TUBULIN BETA-4 CHAIN 1 184 1.6E-117
3 g5213.t2 PANTHER PTHR11588 TUBULIN 1 184 1.6E-117
7 g5213.t2 PRINTS PR01163 Beta-tubulin signature 9 25 4.6E-59
5 g5213.t2 PRINTS PR01163 Beta-tubulin signature 55 73 4.6E-59
8 g5213.t2 PRINTS PR01163 Beta-tubulin signature 73 87 4.6E-59
9 g5213.t2 PRINTS PR01163 Beta-tubulin signature 91 114 4.6E-59
4 g5213.t2 PRINTS PR01163 Beta-tubulin signature 121 132 4.6E-59
6 g5213.t2 PRINTS PR01163 Beta-tubulin signature 156 174 4.6E-59
1 g5213.t2 Pfam PF03953 Tubulin C-terminal domain 5 126 1.5E-43
14 g5213.t2 SMART SM00865 Tubulin_C_4 1 127 4.0E-37
10 g5213.t2 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 1 173 1.59E-77

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5213/g5213.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5213.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005874 microtubule CC
GO:0007017 microtubule-based process BP
GO:0005525 GTP binding MF
GO:0005200 structural constituent of cytoskeleton MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values