Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin beta-1 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_1 g13912 g13912.t7 TTS g13912.t7 33362101 33362101
chr_1 g13912 g13912.t7 isoform g13912.t7 33362785 33363638
chr_1 g13912 g13912.t7 exon g13912.t7.exon1 33362785 33363638
chr_1 g13912 g13912.t7 cds g13912.t7.CDS1 33362786 33363613
chr_1 g13912 g13912.t7 TSS g13912.t7 NA NA

Sequences

>g13912.t7 Gene=g13912 Length=854
TCTCGGAGGTGGTACAGGTTCAGGAATGGGAACACTTTTGATTTCAAAGATTCGTGAAGA
ATATCCAGATCGTATTATGAACACCTATTCAGTGGTGCCATCACCAAAAGTATCAGACAC
AGTCGTTGAGCCCTACAATGCAACACTTTCAGTGCACCAGCTCGTCGAAAACACAGATGA
AACATACTGTATTGACAATGAAGCTCTCTATGATATCTGTTTCCGCACACTCAAACTTAC
CACACCAACATACGGTGATCTCAATCATCTCGTCTCACTTACCATGTCTGGTGTCACTAC
CTGCCTTCGTTTTCCTGGTCAACTGAACGCTGATTTGCGTAAATTGGCTGTCAACATGGT
TCCATTCCCGCGTCTTCACTTCTTCATGCCAGGTTTTGCTCCACTCACATCACGTGGCTC
ACAACAGTATCGTGCATTGACAGTTCCAGAATTGACACAACAAATGTTTGATGCCAAGAA
TATGATGGCTGCCTGTGATCCAAGACATGGTCGTTATCTCACAGTCGCTGCTGTTTTTCG
TGGACGTATGTCAATGAAGGAAGTCGACGAACAAATGCTTAACATTCAAAACAAGAACAG
CAGTTACTTCGTCGAATGGATTCCAAATAACGTCAAGACAGCCGTTTGTGACATTCCACC
ACGTGGTCTCAAAATGAGTGCTACATTCATCGGTAACTCAACTGCCATCCAAGAACTCTT
CAAGCGCATTTCAGAACAATTCACTGCTATGTTCCGTCGTAAAGCTTTCTTGCATTGGTA
CACTGGTGAAGGTATGGACGAAATGGAATTCACAGAAGCTGAAAGCAACATGAACGATCT
TGTTAGCGAATACC

>g13912.t7 Gene=g13912 Length=276
MGTLLISKIREEYPDRIMNTYSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEA
LYDICFRTLKLTTPTYGDLNHLVSLTMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFF
MPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEV
DEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFT
AMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g13912.t7 CDD cd02187 beta_tubulin 1 276 0
24 g13912.t7 Gene3D G3DSA:3.40.50.1440 - 1 117 0
23 g13912.t7 Gene3D G3DSA:3.30.1330.20 - 118 227 0
22 g13912.t7 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 228 276 0
3 g13912.t7 PANTHER PTHR11588:SF89 TUBULIN BETA CHAIN 1 276 0
4 g13912.t7 PANTHER PTHR11588 TUBULIN 1 276 0
15 g13912.t7 PRINTS PR01161 Tubulin signature 5 26 0
12 g13912.t7 PRINTS PR01163 Beta-tubulin signature 6 18 0
17 g13912.t7 PRINTS PR01161 Tubulin signature 30 43 0
16 g13912.t7 PRINTS PR01161 Tubulin signature 44 64 0
8 g13912.t7 PRINTS PR01163 Beta-tubulin signature 66 78 0
10 g13912.t7 PRINTS PR01163 Beta-tubulin signature 84 93 0
11 g13912.t7 PRINTS PR01163 Beta-tubulin signature 99 112 0
13 g13912.t7 PRINTS PR01163 Beta-tubulin signature 119 135 0
6 g13912.t7 PRINTS PR01163 Beta-tubulin signature 165 183 0
5 g13912.t7 PRINTS PR01163 Beta-tubulin signature 183 197 0
14 g13912.t7 PRINTS PR01163 Beta-tubulin signature 201 224 0
18 g13912.t7 PRINTS PR01161 Tubulin signature 224 252 0
7 g13912.t7 PRINTS PR01163 Beta-tubulin signature 231 242 0
9 g13912.t7 PRINTS PR01163 Beta-tubulin signature 266 276 0
1 g13912.t7 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 2 65 0
2 g13912.t7 Pfam PF03953 Tubulin C-terminal domain 115 236 0
21 g13912.t7 SMART SM00865 Tubulin_C_4 100 237 0
19 g13912.t7 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 97 0
20 g13912.t7 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 98 276 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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
GO:0003924 GTPase activity 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