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_1 g13911 g13911.t6 TSS g13911.t6 33336899 33336899
chr_1 g13911 g13911.t6 isoform g13911.t6 33337091 33337971
chr_1 g13911 g13911.t6 exon g13911.t6.exon1 33337091 33337971
chr_1 g13911 g13911.t6 cds g13911.t6.CDS1 33337156 33337971
chr_1 g13911 g13911.t6 TTS g13911.t6 33338892 33338892

Sequences

>g13911.t6 Gene=g13911 Length=881
CTTCGCGTTCTTCGGGTGGCAAGTATGTGCCAAGAGCCATTCTTTTGGATCTTGAGCCTG
GCACTATGGAAGCTGTTCGTTGTGGCGCCTATGGAAAACTTTTCCGACCAGATAACTTTG
TTTTCGGTCAATCTGGTGCTGGTAACAATTGGGCAAAGGGTCATTACACTGAAGGAGCCG
AACTCGTAGATGCTGTTTTGGATGTTGTTCGCAAAGAGTGCGAAAATTGCGATTGTTTAC
AAGGATTCCAATTGACACATTCTCTCGGAGGTGGTACAGGTTCAGGAATGGGAACACTTT
TGATTTCAAAGATTCGTGAAGAATATCCAGATCGTATTATGAACACCTATTCAGTTCTTC
CTTCACCTAAGGTCTCTGATACTGTCGTTGAGCCTTACAATGCAACACTCAGTATTCATC
AATTGGTTGAAAATACTGATGAAACTTATTGCATTGACAATGAAGCTCTTTATGATATTT
GCTTCCGTACATTGAAGGTTCCTAATCCAAGTTATGGCGACCTTAATCATCTCGTCTCAC
TTACCATGTCTGGTGTCACTACCTGCCTTCGTTTTCCTGGTCAACTGAACGCTGATTTGC
GTAAATTGGCTGTCAACATGGTTCCATTCCCGCGTCTTCACTTCTTCATGCCAGGTTTTG
CTCCACTCACATCACGTGGCTCACAACAGTATCGTGCATTGACAGTTCCAGAATTGACAC
AACAAATGTTTGATGCCAAGAATATGATGACAGCATGCGATCCAAGACATGGTCGTTATC
TCACAGTCGCTGCCGTTTTCCGTGGACGTATGTCAATGAAGGAAGTCGACGAACAGATGT
TGGCTGTACAAAATAAGAACAGCAGTTACTTCGTCGAATGG

>g13911.t6 Gene=g13911 Length=272
MEAVRCGAYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVVRKECENCDCLQG
FQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTYSVLPSPKVSDTVVEPYNATLSIHQL
VENTDETYCIDNEALYDICFRTLKVPNPSYGDLNHLVSLTMSGVTTCLRFPGQLNADLRK
LAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMTACDPRHGRYLT
VAAVFRGRMSMKEVDEQMLAVQNKNSSYFVEW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g13911.t6 CDD cd02187 beta_tubulin 1 272 0.0
23 g13911.t6 Gene3D G3DSA:3.40.50.1440 - 1 191 1.4E-87
22 g13911.t6 Gene3D G3DSA:3.30.1330.20 - 192 272 1.4E-40
3 g13911.t6 PANTHER PTHR11588 TUBULIN 1 272 1.3E-195
4 g13911.t6 PANTHER PTHR11588:SF273 TUBULIN BETA-3 CHAIN 1 272 1.3E-195
10 g13911.t6 PRINTS PR01163 Beta-tubulin signature 16 27 4.8E-76
15 g13911.t6 PRINTS PR01161 Tubulin signature 21 32 1.8E-64
18 g13911.t6 PRINTS PR01161 Tubulin signature 34 58 1.8E-64
5 g13911.t6 PRINTS PR01163 Beta-tubulin signature 36 54 4.8E-76
17 g13911.t6 PRINTS PR01161 Tubulin signature 60 78 1.8E-64
19 g13911.t6 PRINTS PR01161 Tubulin signature 79 100 1.8E-64
12 g13911.t6 PRINTS PR01163 Beta-tubulin signature 80 92 4.8E-76
16 g13911.t6 PRINTS PR01161 Tubulin signature 104 117 1.8E-64
14 g13911.t6 PRINTS PR01161 Tubulin signature 118 138 1.8E-64
9 g13911.t6 PRINTS PR01163 Beta-tubulin signature 140 152 4.8E-76
8 g13911.t6 PRINTS PR01163 Beta-tubulin signature 158 167 4.8E-76
7 g13911.t6 PRINTS PR01163 Beta-tubulin signature 173 186 4.8E-76
6 g13911.t6 PRINTS PR01163 Beta-tubulin signature 193 209 4.8E-76
13 g13911.t6 PRINTS PR01163 Beta-tubulin signature 239 257 4.8E-76
11 g13911.t6 PRINTS PR01163 Beta-tubulin signature 257 271 4.8E-76
1 g13911.t6 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 8 139 6.8E-46
2 g13911.t6 Pfam PF03953 Tubulin C-terminal domain 189 272 1.2E-27
25 g13911.t6 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 68 74 -
26 g13911.t6 SMART SM00864 Tubulin_4 1 172 2.4E-48
27 g13911.t6 SMART SM00865 Tubulin_C_4 174 272 1.2E-18
20 g13911.t6 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 3 171 1.96E-69
21 g13911.t6 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 172 272 4.27E-40

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