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 g13965 g13965.t1 TTS g13965.t1 33650201 33650201
chr_1 g13965 g13965.t1 isoform g13965.t1 33650364 33651828
chr_1 g13965 g13965.t1 exon g13965.t1.exon1 33650364 33651386
chr_1 g13965 g13965.t1 cds g13965.t1.CDS1 33650364 33651386
chr_1 g13965 g13965.t1 exon g13965.t1.exon2 33651444 33651695
chr_1 g13965 g13965.t1 cds g13965.t1.CDS2 33651444 33651695
chr_1 g13965 g13965.t1 exon g13965.t1.exon3 33651772 33651828
chr_1 g13965 g13965.t1 cds g13965.t1.CDS3 33651772 33651828
chr_1 g13965 g13965.t1 TSS g13965.t1 33651935 33651935

Sequences

>g13965.t1 Gene=g13965 Length=1332
ATGCGTGAAATTGTTCATATTCAAGCCGGTCAATGCGGAAATCAAATTGGAGCTAAGTTT
TGGGAAGTAATTTCTGACGAGCACTCAATTGATGCTACTGGTTGTTATTGTGGTGATTCT
GATTTGCAATTAGAGCGAATTAATGTCTATTATAATGAAGCAAGTGGTGGAAAATACGTT
CCTCGCGCAATTCTTGTTGATTTGGAGCCTGGAACAATGGATTCAGTAAGAGCAAGTCCA
TTTGGGCAGCTTTTTAGACCAGACAATTTTGTTTTCGGTCAATCAGGTGCTGGTAACAAT
TGGGCAAAGGGTCATTACACTGAAGGAGCTGAACTAGTAGATTCAGTTTTGGATGTTGTC
CGCAAAGAAGCTGAAGGTTGCGACTGTTTACAAGGATTCCAATTGACACATTCACTCGGA
GGTGGTACAGGTTCAGGAATGGGAACACTTTTGATTTCAAAGATTCGTGAAGAATATCCA
GATCGTATTATGAACACCTATTCAGTTGTGCCATCACCAAAAGTGTCAGACACAGTCGTT
GAGCCCTACAATGCAACACTTTCAACTCATCAACTTGTTGAAAATACTGATGAATCGTAT
TGTATCGACAATGAAGCTCTCTATGATATTTGCTTCCGCACTTTGAAACTAACAACACCA
ACATATGGCGATCTTAATCATCTTGTATCAGCAACAATGTCTGGTGTCACTACCTGCCTT
CGTTTTCCTGGTCAACTGAACGCTGATTTGCGTAAATTGGCTGTCAACATGGTTCCATTC
CCGCGTCTTCACTTCTTCATGACTGGCTTTGCTCCACTCACATCACGTGGCTCACAACAG
TATCGTGCATTGACAGTTCCTGAGTTAACTCAACAATTATTTGATTCAAAAAATATGATG
GCCGCCTGTGATCCAAGACATGGGCGTTATTTAACAGTAGCAACAGTTTTCCGTGGACGC
ATGTCAATGAAGGAAGTCGACGAACAAATGATGAATATACAACAGAAAAACAATAGCTAT
TTCGTTGAATGGATTCCAAATAATGTCAAGACAGCCGTTTGCGACATTCCGCCACGTGGT
CTCAAAATGAGTGCTACATTTATCGGTAATTCAACTGCCATCCAAGAACTTTTTAAACGC
ATTGCAGAGCAATTCACTGCTATGTTCCGCCGTAAAGCTTTCTTGCATTGGTACACTGGT
GAAGGTATGGACGAAATGGAATTTACAGAAGCTGAAAGTAACATGAACGATTTGGTCAGT
GAATATCAACAATACCAAGAAGCAACTGCCGATGAAGATATCGAAGGAGAAGAAGATGAG
GAAGAGCAATAA

>g13965.t1 Gene=g13965 Length=443
MREIVHIQAGQCGNQIGAKFWEVISDEHSIDATGCYCGDSDLQLERINVYYNEASGGKYV
PRAILVDLEPGTMDSVRASPFGQLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAEGCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTYSVVPSPKVSDTVV
EPYNATLSTHQLVENTDESYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMTGFAPLTSRGSQQYRALTVPELTQQLFDSKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMMNIQQKNNSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRIAEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQEATADEDIEGEEDEEEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
33 g13965.t1 CDD cd02187 beta_tubulin 2 426 0.0
32 g13965.t1 Coils Coil Coil 408 428 -
31 g13965.t1 Gene3D G3DSA:3.40.50.1440 - 1 263 4.3E-126
30 g13965.t1 Gene3D G3DSA:3.30.1330.20 - 264 373 7.7E-57
29 g13965.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 374 443 2.3E-34
39 g13965.t1 MobiDBLite mobidb-lite consensus disorder prediction 424 443 -
38 g13965.t1 MobiDBLite mobidb-lite consensus disorder prediction 428 443 -
3 g13965.t1 PANTHER PTHR11588:SF314 TUBULIN BETA-2 CHAIN 1 437 0.0
4 g13965.t1 PANTHER PTHR11588 TUBULIN 1 437 0.0
19 g13965.t1 PRINTS PR01161 Tubulin signature 10 30 5.5E-104
9 g13965.t1 PRINTS PR01163 Beta-tubulin signature 41 58 3.2E-121
26 g13965.t1 PRINTS PR01161 Tubulin signature 51 70 5.5E-104
11 g13965.t1 PRINTS PR01163 Beta-tubulin signature 88 99 3.2E-121
22 g13965.t1 PRINTS PR01161 Tubulin signature 93 104 5.5E-104
23 g13965.t1 PRINTS PR01161 Tubulin signature 106 130 5.5E-104
14 g13965.t1 PRINTS PR01163 Beta-tubulin signature 108 126 3.2E-121
24 g13965.t1 PRINTS PR01161 Tubulin signature 132 150 5.5E-104
25 g13965.t1 PRINTS PR01161 Tubulin signature 151 172 5.5E-104
6 g13965.t1 PRINTS PR01163 Beta-tubulin signature 152 164 3.2E-121
21 g13965.t1 PRINTS PR01161 Tubulin signature 176 189 5.5E-104
20 g13965.t1 PRINTS PR01161 Tubulin signature 190 210 5.5E-104
17 g13965.t1 PRINTS PR01163 Beta-tubulin signature 212 224 3.2E-121
8 g13965.t1 PRINTS PR01163 Beta-tubulin signature 230 239 3.2E-121
7 g13965.t1 PRINTS PR01163 Beta-tubulin signature 245 258 3.2E-121
16 g13965.t1 PRINTS PR01163 Beta-tubulin signature 265 281 3.2E-121
10 g13965.t1 PRINTS PR01163 Beta-tubulin signature 311 329 3.2E-121
15 g13965.t1 PRINTS PR01163 Beta-tubulin signature 329 343 3.2E-121
5 g13965.t1 PRINTS PR01163 Beta-tubulin signature 347 370 3.2E-121
18 g13965.t1 PRINTS PR01161 Tubulin signature 370 398 5.5E-104
13 g13965.t1 PRINTS PR01163 Beta-tubulin signature 377 388 3.2E-121
12 g13965.t1 PRINTS PR01163 Beta-tubulin signature 412 430 3.2E-121
1 g13965.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 211 2.3E-68
2 g13965.t1 Pfam PF03953 Tubulin C-terminal domain 261 382 8.0E-43
36 g13965.t1 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
37 g13965.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
34 g13965.t1 SMART SM00864 Tubulin_4 47 244 1.3E-70
35 g13965.t1 SMART SM00865 Tubulin_C_4 246 383 4.8E-51
27 g13965.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 243 7.06E-102
28 g13965.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 244 429 4.27E-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

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