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.t3 TTS g13912.t3 33362101 33362101
chr_1 g13912 g13912.t3 isoform g13912.t3 33362216 33366435
chr_1 g13912 g13912.t3 exon g13912.t3.exon1 33362216 33362222
chr_1 g13912 g13912.t3 exon g13912.t3.exon2 33362280 33363994
chr_1 g13912 g13912.t3 cds g13912.t3.CDS1 33362708 33363994
chr_1 g13912 g13912.t3 exon g13912.t3.exon3 33366379 33366435
chr_1 g13912 g13912.t3 cds g13912.t3.CDS2 33366379 33366435
chr_1 g13912 g13912.t3 TSS g13912.t3 33366633 33366633

Sequences

>g13912.t3 Gene=g13912 Length=1779
ATGCGTGAAATCGTTCATATTCAAGCTGGTCAATGCGGAAACCAAATTGGAGCAAAGTTT
TGGGAAATTATTTCTGATGAGCATGGAATTGACGCAACTGGCGCCTATCATGGCGATTCT
GACTTGCAATTAGAGCGCATCAATGTCTACTATAATGAGGCATCAGGTGGCAAATACGTT
CCACGTGCTGTTTTGGTTGATTTGGAACCAGGTACTATGGATTCAGTTCGTTCTGGTCCA
TTTGGTCAGATTTTCCGACCAGACAACTTTGTTTTCGGTCAATCTGGTGCTGGTAACAAT
TGGGCAAAGGGTCATTACACTGAAGGAGCCGAACTCGTAGATTCAGTTTTGGATGTTGTC
CGCAAAGAAGCTGAGTCATGCGATTGTTTACAAGGATTCCAATTGACACATTCTCTCGGA
GGTGGTACAGGTTCAGGAATGGGAACACTTTTGATTTCAAAGATTCGTGAAGAATATCCA
GATCGTATTATGAACACCTATTCAGTGGTGCCATCACCAAAAGTATCAGACACAGTCGTT
GAGCCCTACAATGCAACACTTTCAGTGCACCAGCTCGTCGAAAACACAGATGAAACATAC
TGTATTGACAATGAAGCTCTCTATGATATCTGTTTCCGCACACTCAAACTTACCACACCA
ACATACGGTGATCTCAATCATCTCGTCTCACTTACCATGTCTGGTGTCACTACCTGCCTT
CGTTTTCCTGGTCAACTGAACGCTGATTTGCGTAAATTGGCTGTCAACATGGTTCCATTC
CCGCGTCTTCACTTCTTCATGCCAGGTTTTGCTCCACTCACATCACGTGGCTCACAACAG
TATCGTGCATTGACAGTTCCAGAATTGACACAACAAATGTTTGATGCCAAGAATATGATG
GCTGCCTGTGATCCAAGACATGGTCGTTATCTCACAGTCGCTGCTGTTTTTCGTGGACGT
ATGTCAATGAAGGAAGTCGACGAACAAATGCTTAACATTCAAAACAAGAACAGCAGTTAC
TTCGTCGAATGGATTCCAAATAACGTCAAGACAGCCGTTTGTGACATTCCACCACGTGGT
CTCAAAATGAGTGCTACATTCATCGGTAACTCAACTGCCATCCAAGAACTCTTCAAGCGC
ATTTCAGAACAATTCACTGCTATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACACTGGT
GAAGGTATGGACGAAATGGAATTCACAGAAGCTGAAAGCAACATGAACGATCTTGTTAGC
GAATACCAACAATACCAAGAAGCAACTGCTGACGAAGATGCCGAATTCGATGAAGAACAA
GAAGCTGAAGTTGATGAAGCTTAAGCTGCTTATCTTTATTTAATAAGAATAAAAATGTTT
CTCCTATTACTCCCTGATAAAAAACTTTAATTCCCTTCAGAACACTATTTGCAAAAAATG
AAAGAATGCTTTTTAAATGTGTAACACACTGCCTATTCCTATTGTCTTTATTCTGAATCA
ATAATCAAAAAATTAAAAACTCTCTGTGAAAAAAATTGTTCTTATAAAAAAGTAAATTTG
TGTTTTTCGTTCACAAAAAAATTTATTGATTGATACACATGTCTCTTAATAACTTTTTAA
AAACAATTGATTAACACAACAAAAATATTTCCATATACACAACACAATACCACTCAATGT
TGATGTAATTTTGTTCTTTTTTTTGTTAAATACAATAGTTTTTCGAATTCGCATGAAACC
AATATTTTTCCTTTACAATCCTTTTCTCCTATTTTATCA

>g13912.t3 Gene=g13912 Length=447
MREIVHIQAGQCGNQIGAKFWEIISDEHGIDATGAYHGDSDLQLERINVYYNEASGGKYV
PRAVLVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTYSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSLTMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQEATADEDAEFDEEQEAEVDEA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
33 g13912.t3 CDD cd02187 beta_tubulin 2 426 0.0
32 g13912.t3 Coils Coil Coil 408 428 -
31 g13912.t3 Gene3D G3DSA:3.40.50.1440 - 1 263 1.1E-126
30 g13912.t3 Gene3D G3DSA:3.30.1330.20 - 264 373 7.3E-58
29 g13912.t3 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 374 445 2.7E-35
39 g13912.t3 MobiDBLite mobidb-lite consensus disorder prediction 427 447 -
38 g13912.t3 MobiDBLite mobidb-lite consensus disorder prediction 428 447 -
3 g13912.t3 PANTHER PTHR11588:SF314 TUBULIN BETA-2 CHAIN 1 441 0.0
4 g13912.t3 PANTHER PTHR11588 TUBULIN 1 441 0.0
19 g13912.t3 PRINTS PR01161 Tubulin signature 10 30 3.8E-105
9 g13912.t3 PRINTS PR01163 Beta-tubulin signature 41 58 5.8E-123
26 g13912.t3 PRINTS PR01161 Tubulin signature 51 70 3.8E-105
11 g13912.t3 PRINTS PR01163 Beta-tubulin signature 88 99 5.8E-123
22 g13912.t3 PRINTS PR01161 Tubulin signature 93 104 3.8E-105
23 g13912.t3 PRINTS PR01161 Tubulin signature 106 130 3.8E-105
14 g13912.t3 PRINTS PR01163 Beta-tubulin signature 108 126 5.8E-123
24 g13912.t3 PRINTS PR01161 Tubulin signature 132 150 3.8E-105
25 g13912.t3 PRINTS PR01161 Tubulin signature 151 172 3.8E-105
6 g13912.t3 PRINTS PR01163 Beta-tubulin signature 152 164 5.8E-123
21 g13912.t3 PRINTS PR01161 Tubulin signature 176 189 3.8E-105
20 g13912.t3 PRINTS PR01161 Tubulin signature 190 210 3.8E-105
17 g13912.t3 PRINTS PR01163 Beta-tubulin signature 212 224 5.8E-123
8 g13912.t3 PRINTS PR01163 Beta-tubulin signature 230 239 5.8E-123
7 g13912.t3 PRINTS PR01163 Beta-tubulin signature 245 258 5.8E-123
16 g13912.t3 PRINTS PR01163 Beta-tubulin signature 265 281 5.8E-123
10 g13912.t3 PRINTS PR01163 Beta-tubulin signature 311 329 5.8E-123
15 g13912.t3 PRINTS PR01163 Beta-tubulin signature 329 343 5.8E-123
5 g13912.t3 PRINTS PR01163 Beta-tubulin signature 347 370 5.8E-123
18 g13912.t3 PRINTS PR01161 Tubulin signature 370 398 3.8E-105
13 g13912.t3 PRINTS PR01163 Beta-tubulin signature 377 388 5.8E-123
12 g13912.t3 PRINTS PR01163 Beta-tubulin signature 412 430 5.8E-123
1 g13912.t3 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 211 8.9E-69
2 g13912.t3 Pfam PF03953 Tubulin C-terminal domain 261 382 1.3E-42
36 g13912.t3 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
37 g13912.t3 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
34 g13912.t3 SMART SM00864 Tubulin_4 47 244 3.2E-69
35 g13912.t3 SMART SM00865 Tubulin_C_4 246 383 5.6E-51
27 g13912.t3 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 243 3.14E-102
28 g13912.t3 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 244 429 6.71E-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

Pathway

  • This transcript belongs to the following pathways

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