Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin beta 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 g13965 g13965.t2 TTS g13965.t2 33650201 33650201
chr_1 g13965 g13965.t2 isoform g13965.t2 33650364 33651828
chr_1 g13965 g13965.t2 exon g13965.t2.exon1 33650364 33651386
chr_1 g13965 g13965.t2 cds g13965.t2.CDS1 33650364 33651257
chr_1 g13965 g13965.t2 exon g13965.t2.exon2 33651461 33651695
chr_1 g13965 g13965.t2 exon g13965.t2.exon3 33651772 33651828
chr_1 g13965 g13965.t2 TSS g13965.t2 33651935 33651935

Sequences

>g13965.t2 Gene=g13965 Length=1315
ATGCGTGAAATTGTTCATATTCAAGCCGGTCAATGCGGAAATCAAATTGGAGCTAAGTTT
TGGGAAGTAATTTCTGACGAGCACTCAATTGATGCTACTGGTTGTTATTGTGGTGATTCT
GATTTGCAATTAGAGCGAATTAATGTCTATTATAATGAAGCAAGTGGTGGAAAATACGTT
CCTCGCGCAATTCTTGTTGATTTGGAGCCTGGAACAATGGATTCAGTAAGAGCAAGTCCA
TTTGGGCAGCTTTTTAGACCAGACAATTTTGTTTTCGGTCAATCAGGTGCTGGGTCATTA
CACTGAAGGAGCTGAACTAGTAGATTCAGTTTTGGATGTTGTCCGCAAAGAAGCTGAAGG
TTGCGACTGTTTACAAGGATTCCAATTGACACATTCACTCGGAGGTGGTACAGGTTCAGG
AATGGGAACACTTTTGATTTCAAAGATTCGTGAAGAATATCCAGATCGTATTATGAACAC
CTATTCAGTTGTGCCATCACCAAAAGTGTCAGACACAGTCGTTGAGCCCTACAATGCAAC
ACTTTCAACTCATCAACTTGTTGAAAATACTGATGAATCGTATTGTATCGACAATGAAGC
TCTCTATGATATTTGCTTCCGCACTTTGAAACTAACAACACCAACATATGGCGATCTTAA
TCATCTTGTATCAGCAACAATGTCTGGTGTCACTACCTGCCTTCGTTTTCCTGGTCAACT
GAACGCTGATTTGCGTAAATTGGCTGTCAACATGGTTCCATTCCCGCGTCTTCACTTCTT
CATGACTGGCTTTGCTCCACTCACATCACGTGGCTCACAACAGTATCGTGCATTGACAGT
TCCTGAGTTAACTCAACAATTATTTGATTCAAAAAATATGATGGCCGCCTGTGATCCAAG
ACATGGGCGTTATTTAACAGTAGCAACAGTTTTCCGTGGACGCATGTCAATGAAGGAAGT
CGACGAACAAATGATGAATATACAACAGAAAAACAATAGCTATTTCGTTGAATGGATTCC
AAATAATGTCAAGACAGCCGTTTGCGACATTCCGCCACGTGGTCTCAAAATGAGTGCTAC
ATTTATCGGTAATTCAACTGCCATCCAAGAACTTTTTAAACGCATTGCAGAGCAATTCAC
TGCTATGTTCCGCCGTAAAGCTTTCTTGCATTGGTACACTGGTGAAGGTATGGACGAAAT
GGAATTTACAGAAGCTGAAAGTAACATGAACGATTTGGTCAGTGAATATCAACAATACCA
AGAAGCAACTGCCGATGAAGATATCGAAGGAGAAGAAGATGAGGAAGAGCAATAA

>g13965.t2 Gene=g13965 Length=297
MGTLLISKIREEYPDRIMNTYSVVPSPKVSDTVVEPYNATLSTHQLVENTDESYCIDNEA
LYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFF
MTGFAPLTSRGSQQYRALTVPELTQQLFDSKNMMAACDPRHGRYLTVATVFRGRMSMKEV
DEQMMNIQQKNNSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRIAEQFT
AMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQEATADEDIEGEEDEEEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g13965.t2 CDD cd02187 beta_tubulin 1 280 0.0
24 g13965.t2 Coils Coil Coil 262 282 -
23 g13965.t2 Gene3D G3DSA:3.40.50.1440 - 1 116 2.0E-45
22 g13965.t2 Gene3D G3DSA:3.30.1330.20 - 117 227 3.5E-57
21 g13965.t2 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 228 297 1.2E-34
27 g13965.t2 MobiDBLite mobidb-lite consensus disorder prediction 278 297 -
28 g13965.t2 MobiDBLite mobidb-lite consensus disorder prediction 282 297 -
3 g13965.t2 PANTHER PTHR11588:SF89 TUBULIN BETA CHAIN 1 290 3.1E-203
4 g13965.t2 PANTHER PTHR11588 TUBULIN 1 290 3.1E-203
15 g13965.t2 PRINTS PR01161 Tubulin signature 5 26 5.4E-43
12 g13965.t2 PRINTS PR01163 Beta-tubulin signature 6 18 3.6E-91
17 g13965.t2 PRINTS PR01161 Tubulin signature 30 43 5.4E-43
16 g13965.t2 PRINTS PR01161 Tubulin signature 44 64 5.4E-43
8 g13965.t2 PRINTS PR01163 Beta-tubulin signature 66 78 3.6E-91
9 g13965.t2 PRINTS PR01163 Beta-tubulin signature 84 93 3.6E-91
10 g13965.t2 PRINTS PR01163 Beta-tubulin signature 99 112 3.6E-91
13 g13965.t2 PRINTS PR01163 Beta-tubulin signature 119 135 3.6E-91
6 g13965.t2 PRINTS PR01163 Beta-tubulin signature 165 183 3.6E-91
5 g13965.t2 PRINTS PR01163 Beta-tubulin signature 183 197 3.6E-91
14 g13965.t2 PRINTS PR01163 Beta-tubulin signature 201 224 3.6E-91
18 g13965.t2 PRINTS PR01161 Tubulin signature 224 252 5.4E-43
7 g13965.t2 PRINTS PR01163 Beta-tubulin signature 231 242 3.6E-91
11 g13965.t2 PRINTS PR01163 Beta-tubulin signature 266 284 3.6E-91
1 g13965.t2 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 2 65 6.1E-14
2 g13965.t2 Pfam PF03953 Tubulin C-terminal domain 115 236 3.5E-43
26 g13965.t2 SMART SM00865 Tubulin_C_4 100 237 4.8E-51
19 g13965.t2 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 97 9.81E-33
20 g13965.t2 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 98 283 1.46E-84

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. There were no conditions that were differentially expressed