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_3 g134 g134.t1 isoform g134.t1 1239637 1242298
chr_3 g134 g134.t1 exon g134.t1.exon1 1239637 1239693
chr_3 g134 g134.t1 cds g134.t1.CDS1 1239637 1239693
chr_3 g134 g134.t1 exon g134.t1.exon2 1240915 1241185
chr_3 g134 g134.t1 cds g134.t1.CDS2 1240915 1241185
chr_3 g134 g134.t1 exon g134.t1.exon3 1241271 1242298
chr_3 g134 g134.t1 cds g134.t1.CDS3 1241271 1242298
chr_3 g134 g134.t1 TSS g134.t1 NA NA
chr_3 g134 g134.t1 TTS g134.t1 NA NA

Sequences

>g134.t1 Gene=g134 Length=1356
ATGCGTGAAATTGTTCATATTCAAGCAGGACAATGTGGAAATCAAATTGGTGCTAAATTT
TGGGAAATAATTTCGGATGAGCATGGCATTGATGCGACTGGAAATTATATAGGCGATTCT
GATCTTCAACTGGAGCGTATCAATGTTTATTACAATGAAGCAACTGGCGGCACAAAATTT
GTTCCTCGTGCGATTCTTATTGATCTTGAACCTGGTACAATTGAAAGTTTACGAATGTCA
TCAATTGGCAGACTTTTTAGACCAGATAATTTTGTATTTGGACAATCGGGTGCTGGAAAT
AATTGGGCAAAAGGTCATTATACCGAAGGTGCCGAGCTCGTAGATTCAGTTTTAGATGTT
GTTCGTAAAGAAACTGAAGGTTGTGATTGCTTGCAAGGTTTCCAGCTTACTCATTCACTT
GGTGGTGGAACAGGAAGCGGAATGGGAACACTTTTAATTTCAAAAATACGTGAAGAATAT
CCTGATCGTATTATGAACACTTTCTCTGTCGTTCCTTCACCTAAAGTCTCTGATACTGTC
GTTGAACCTTACAATTCTACACTCAGTATTCATCAGCTTGTTGAAAATACCGATGAGACT
TTCTGTATCGATAACGAAGCACTTTATGACATTTGTTTCCGAACATTAAAGCTTGTCACA
CCCACATATGGTGACCTCAATCATCTCGTATCACTTACAATGAGCGGTGTTACAACATGC
TTACGTTTTCCAGGTCAACTTAATGCTGATTTACGTAAGCTTGCTGTCAACATGGTGCCA
TTCCCACGTCTTCATTTCTTTATGCCCGGGTTTGCGCCACTATCTGCACGTAGCAGTCAA
CAATATCGTTCACTTTCAGTGCCAGAACTTGCACAACAAATGTTTGATACAAAAAATATG
ATGGCAGCTTGTGATCCAAGACATGGAAGATATTTAACTGTTGCTGCTGTCTTTCGTGGT
CGAATGTCAATGAAAGAAATTGATGAACAAATGCTGACAATTCAAAATAAAAATAGCAGT
TATTTTGTTGAATGGATACCAAGTAATGTCAAGACTGCAGTTTGTGACATTCCACCAAAA
GGATTAAAAATGAGTGCAACATTCATTGGAAACTCAACTGCCATTCAAGAACTATTTCGT
AGAATTTCAGAACAATTTACTTGCATGTTTCGTCGCAAAGCTTTCTTACATTGGTACACA
AGTGAAGGAATGGATGAAATGGAATTCACAGAAGCTGAAAGTAACATGAATGACTTAATT
TCTGAATATCAACAATATCAAGAAGCAACAGCAGATGAATATGCAGAATTTGATGAATCA
AAAATGATGAGAACAGAAAAAGAGTTTGATGGTTAA

>g134.t1 Gene=g134 Length=451
MREIVHIQAGQCGNQIGAKFWEIISDEHGIDATGNYIGDSDLQLERINVYYNEATGGTKF
VPRAILIDLEPGTIESLRMSSIGRLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDV
VRKETEGCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTV
VEPYNSTLSIHQLVENTDETFCIDNEALYDICFRTLKLVTPTYGDLNHLVSLTMSGVTTC
LRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLSARSSQQYRSLSVPELAQQMFDTKNM
MAACDPRHGRYLTVAAVFRGRMSMKEIDEQMLTIQNKNSSYFVEWIPSNVKTAVCDIPPK
GLKMSATFIGNSTAIQELFRRISEQFTCMFRRKAFLHWYTSEGMDEMEFTEAESNMNDLI
SEYQQYQEATADEYAEFDESKMMRTEKEFDG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
33 g134.t1 CDD cd02187 beta_tubulin 2 427 0.0
32 g134.t1 Coils Coil Coil 409 429 -
31 g134.t1 Gene3D G3DSA:3.40.50.1440 - 1 264 4.1E-121
30 g134.t1 Gene3D G3DSA:3.30.1330.20 - 265 374 8.8E-55
29 g134.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 375 444 8.9E-33
3 g134.t1 PANTHER PTHR11588:SF314 TUBULIN BETA-2 CHAIN 1 442 7.8E-294
4 g134.t1 PANTHER PTHR11588 TUBULIN 1 442 7.8E-294
22 g134.t1 PRINTS PR01161 Tubulin signature 10 30 2.9E-100
10 g134.t1 PRINTS PR01163 Beta-tubulin signature 41 58 8.6E-117
21 g134.t1 PRINTS PR01161 Tubulin signature 52 71 2.9E-100
14 g134.t1 PRINTS PR01163 Beta-tubulin signature 89 100 8.6E-117
24 g134.t1 PRINTS PR01161 Tubulin signature 94 105 2.9E-100
26 g134.t1 PRINTS PR01161 Tubulin signature 107 131 2.9E-100
6 g134.t1 PRINTS PR01163 Beta-tubulin signature 109 127 8.6E-117
20 g134.t1 PRINTS PR01161 Tubulin signature 133 151 2.9E-100
18 g134.t1 PRINTS PR01161 Tubulin signature 152 173 2.9E-100
13 g134.t1 PRINTS PR01163 Beta-tubulin signature 153 165 8.6E-117
19 g134.t1 PRINTS PR01161 Tubulin signature 177 190 2.9E-100
25 g134.t1 PRINTS PR01161 Tubulin signature 191 211 2.9E-100
12 g134.t1 PRINTS PR01163 Beta-tubulin signature 213 225 8.6E-117
9 g134.t1 PRINTS PR01163 Beta-tubulin signature 231 240 8.6E-117
8 g134.t1 PRINTS PR01163 Beta-tubulin signature 246 259 8.6E-117
15 g134.t1 PRINTS PR01163 Beta-tubulin signature 266 282 8.6E-117
17 g134.t1 PRINTS PR01163 Beta-tubulin signature 312 330 8.6E-117
7 g134.t1 PRINTS PR01163 Beta-tubulin signature 330 344 8.6E-117
11 g134.t1 PRINTS PR01163 Beta-tubulin signature 348 371 8.6E-117
23 g134.t1 PRINTS PR01161 Tubulin signature 371 399 2.9E-100
5 g134.t1 PRINTS PR01163 Beta-tubulin signature 378 389 8.6E-117
16 g134.t1 PRINTS PR01163 Beta-tubulin signature 413 431 8.6E-117
1 g134.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 212 2.0E-68
2 g134.t1 Pfam PF03953 Tubulin C-terminal domain 262 383 4.8E-41
34 g134.t1 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
35 g134.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 141 147 -
36 g134.t1 SMART SM00864 Tubulin_4 47 245 3.3E-67
37 g134.t1 SMART SM00865 Tubulin_C_4 247 384 7.9E-49
27 g134.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 244 4.71E-98
28 g134.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 245 430 1.31E-81

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. There were no conditions that were differentially expressed