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.t4 TTS g13912.t4 33362101 33362101
chr_1 g13912 g13912.t4 isoform g13912.t4 33362708 33366435
chr_1 g13912 g13912.t4 exon g13912.t4.exon1 33362708 33363994
chr_1 g13912 g13912.t4 cds g13912.t4.CDS1 33362708 33363835
chr_1 g13912 g13912.t4 exon g13912.t4.exon2 33366375 33366435
chr_1 g13912 g13912.t4 TSS g13912.t4 33366633 33366633

Sequences

>g13912.t4 Gene=g13912 Length=1348
ATGCGTGAAATCGTTCATATTCAAGCTGGTCAATGCGGAAACCAAATTGGAGCAAAGGTA
TTTTTGGGAAATTATTTCTGATGAGCATGGAATTGACGCAACTGGCGCCTATCATGGCGA
TTCTGACTTGCAATTAGAGCGCATCAATGTCTACTATAATGAGGCATCAGGTGGCAAATA
CGTTCCACGTGCTGTTTTGGTTGATTTGGAACCAGGTACTATGGATTCAGTTCGTTCTGG
TCCATTTGGTCAGATTTTCCGACCAGACAACTTTGTTTTCGGTCAATCTGGTGCTGGTAA
CAATTGGGCAAAGGGTCATTACACTGAAGGAGCCGAACTCGTAGATTCAGTTTTGGATGT
TGTCCGCAAAGAAGCTGAGTCATGCGATTGTTTACAAGGATTCCAATTGACACATTCTCT
CGGAGGTGGTACAGGTTCAGGAATGGGAACACTTTTGATTTCAAAGATTCGTGAAGAATA
TCCAGATCGTATTATGAACACCTATTCAGTGGTGCCATCACCAAAAGTATCAGACACAGT
CGTTGAGCCCTACAATGCAACACTTTCAGTGCACCAGCTCGTCGAAAACACAGATGAAAC
ATACTGTATTGACAATGAAGCTCTCTATGATATCTGTTTCCGCACACTCAAACTTACCAC
ACCAACATACGGTGATCTCAATCATCTCGTCTCACTTACCATGTCTGGTGTCACTACCTG
CCTTCGTTTTCCTGGTCAACTGAACGCTGATTTGCGTAAATTGGCTGTCAACATGGTTCC
ATTCCCGCGTCTTCACTTCTTCATGCCAGGTTTTGCTCCACTCACATCACGTGGCTCACA
ACAGTATCGTGCATTGACAGTTCCAGAATTGACACAACAAATGTTTGATGCCAAGAATAT
GATGGCTGCCTGTGATCCAAGACATGGTCGTTATCTCACAGTCGCTGCTGTTTTTCGTGG
ACGTATGTCAATGAAGGAAGTCGACGAACAAATGCTTAACATTCAAAACAAGAACAGCAG
TTACTTCGTCGAATGGATTCCAAATAACGTCAAGACAGCCGTTTGTGACATTCCACCACG
TGGTCTCAAAATGAGTGCTACATTCATCGGTAACTCAACTGCCATCCAAGAACTCTTCAA
GCGCATTTCAGAACAATTCACTGCTATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACAC
TGGTGAAGGTATGGACGAAATGGAATTCACAGAAGCTGAAAGCAACATGAACGATCTTGT
TAGCGAATACCAACAATACCAAGAAGCAACTGCTGACGAAGATGCCGAATTCGATGAAGA
ACAAGAAGCTGAAGTTGATGAAGCTTAA

>g13912.t4 Gene=g13912 Length=375
MDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQG
FQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTYSVVPSPKVSDTVVEPYNATLSVHQL
VENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSLTMSGVTTCLRFPGQLNADLRK
LAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLT
VAAVFRGRMSMKEVDEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNST
AIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQEATADE
DAEFDEEQEAEVDEA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
30 g13912.t4 CDD cd02187 beta_tubulin 1 354 0.0
29 g13912.t4 Coils Coil Coil 336 356 -
28 g13912.t4 Gene3D G3DSA:3.40.50.1440 - 1 191 3.4E-88
27 g13912.t4 Gene3D G3DSA:3.30.1330.20 - 192 301 5.2E-58
26 g13912.t4 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 302 373 2.0E-35
34 g13912.t4 MobiDBLite mobidb-lite consensus disorder prediction 355 375 -
35 g13912.t4 MobiDBLite mobidb-lite consensus disorder prediction 356 375 -
3 g13912.t4 PANTHER PTHR11588:SF330 TUBULIN BETA-2B CHAIN 1 368 2.1E-263
4 g13912.t4 PANTHER PTHR11588 TUBULIN 1 368 2.1E-263
11 g13912.t4 PRINTS PR01163 Beta-tubulin signature 16 27 3.2E-112
18 g13912.t4 PRINTS PR01161 Tubulin signature 21 32 1.1E-80
22 g13912.t4 PRINTS PR01161 Tubulin signature 34 58 1.1E-80
6 g13912.t4 PRINTS PR01163 Beta-tubulin signature 36 54 3.2E-112
21 g13912.t4 PRINTS PR01161 Tubulin signature 60 78 1.1E-80
23 g13912.t4 PRINTS PR01161 Tubulin signature 79 100 1.1E-80
14 g13912.t4 PRINTS PR01163 Beta-tubulin signature 80 92 3.2E-112
20 g13912.t4 PRINTS PR01161 Tubulin signature 104 117 1.1E-80
17 g13912.t4 PRINTS PR01161 Tubulin signature 118 138 1.1E-80
10 g13912.t4 PRINTS PR01163 Beta-tubulin signature 140 152 3.2E-112
9 g13912.t4 PRINTS PR01163 Beta-tubulin signature 158 167 3.2E-112
8 g13912.t4 PRINTS PR01163 Beta-tubulin signature 173 186 3.2E-112
7 g13912.t4 PRINTS PR01163 Beta-tubulin signature 193 209 3.2E-112
15 g13912.t4 PRINTS PR01163 Beta-tubulin signature 239 257 3.2E-112
13 g13912.t4 PRINTS PR01163 Beta-tubulin signature 257 271 3.2E-112
12 g13912.t4 PRINTS PR01163 Beta-tubulin signature 275 298 3.2E-112
19 g13912.t4 PRINTS PR01161 Tubulin signature 298 326 1.1E-80
16 g13912.t4 PRINTS PR01163 Beta-tubulin signature 305 316 3.2E-112
5 g13912.t4 PRINTS PR01163 Beta-tubulin signature 340 358 3.2E-112
1 g13912.t4 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 139 2.5E-45
2 g13912.t4 Pfam PF03953 Tubulin C-terminal domain 189 310 9.5E-43
33 g13912.t4 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 68 74 -
31 g13912.t4 SMART SM00864 Tubulin_4 1 172 8.5E-48
32 g13912.t4 SMART SM00865 Tubulin_C_4 174 311 5.6E-51
24 g13912.t4 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 171 8.11E-70
25 g13912.t4 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 172 357 4.58E-85

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