Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin beta-3 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 g13911 g13911.t1 TSS g13911.t1 33305581 33305581
chr_1 g13911 g13911.t1 isoform g13911.t1 33305787 33338286
chr_1 g13911 g13911.t1 exon g13911.t1.exon1 33305787 33305843
chr_1 g13911 g13911.t1 cds g13911.t1.CDS1 33305787 33305843
chr_1 g13911 g13911.t1 exon g13911.t1.exon2 33336910 33337018
chr_1 g13911 g13911.t1 cds g13911.t1.CDS2 33336910 33337018
chr_1 g13911 g13911.t1 exon g13911.t1.exon3 33337088 33338286
chr_1 g13911 g13911.t1 cds g13911.t1.CDS3 33337088 33338286
chr_1 g13911 g13911.t1 TTS g13911.t1 33338892 33338892

Sequences

>g13911.t1 Gene=g13911 Length=1365
ATGCGTGAAATCGTTCATTTGCAAGCTGGACAATGTGGTAACCAAATTGGTGCTAAATTT
TGGGAAATTATATCTGAGGAGCATGGTATTGATGCAACCGGTATTTATAAGGGTGAAAGT
GATTTGCAATTGGAACGCGTGAGCGTTTACTATAATGAGGCATCAGCAGCTTCGCGTTCT
TCGGGTGGCAAGTATGTGCCAAGAGCCATTCTTTTGGATCTTGAGCCTGGCACTATGGAA
GCTGTTCGTTGTGGCGCCTATGGAAAACTTTTCCGACCAGATAACTTTGTTTTCGGTCAA
TCTGGTGCTGGTAACAATTGGGCAAAGGGTCATTACACTGAAGGAGCCGAACTCGTAGAT
GCTGTTTTGGATGTTGTTCGCAAAGAGTGCGAAAATTGCGATTGTTTACAAGGATTCCAA
TTGACACATTCTCTCGGAGGTGGTACAGGTTCAGGAATGGGAACACTTTTGATTTCAAAG
ATTCGTGAAGAATATCCAGATCGTATTATGAACACCTATTCAGTTCTTCCTTCACCTAAG
GTCTCTGATACTGTCGTTGAGCCTTACAATGCAACACTCAGTATTCATCAATTGGTTGAA
AATACTGATGAAACTTATTGCATTGACAATGAAGCTCTTTATGATATTTGCTTCCGTACA
TTGAAGGTTCCTAATCCAAGTTATGGCGACCTTAATCATCTCGTCTCACTTACCATGTCT
GGTGTCACTACCTGCCTTCGTTTTCCTGGTCAACTGAACGCTGATTTGCGTAAATTGGCT
GTCAACATGGTTCCATTCCCGCGTCTTCACTTCTTCATGCCAGGTTTTGCTCCACTCACA
TCACGTGGCTCACAACAGTATCGTGCATTGACAGTTCCAGAATTGACACAACAAATGTTT
GATGCCAAGAATATGATGACAGCATGCGATCCAAGACATGGTCGTTATCTCACAGTCGCT
GCCGTTTTCCGTGGACGTATGTCAATGAAGGAAGTCGACGAACAGATGTTGGCTGTACAA
AATAAGAACAGCAGTTACTTCGTCGAATGGATTCCAAATAACGTCAAGACAGCTGTTTGT
GACATTCCACCTAAAGGATTGAAAATGTCATCGACTTTCATTGGAAACACTACTGCCATT
CAAGAACTCTTCAAGCGCATTTCAGAACAATTCTCAGCTATGTTCCGTCGTAAAGCTTTC
TTGCATTGGTACACTGGTGAAGGTATGGACGAAATGGAATTCACAGAAGCTGAAAGCAAC
ATGAACGATCTTGTTAGCGAATACCAACAATACCAAGAAGCAACTGCTGATGATGAATTC
GATGCTGATGTCGATGATGTTGAGCATGATGGCGAATGCGTGTAA

>g13911.t1 Gene=g13911 Length=454
MREIVHLQAGQCGNQIGAKFWEIISEEHGIDATGIYKGESDLQLERVSVYYNEASAASRS
SGGKYVPRAILLDLEPGTMEAVRCGAYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVD
AVLDVVRKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTYSVLPSPK
VSDTVVEPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKVPNPSYGDLNHLVSLTMS
GVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMF
DAKNMMTACDPRHGRYLTVAAVFRGRMSMKEVDEQMLAVQNKNSSYFVEWIPNNVKTAVC
DIPPKGLKMSSTFIGNTTAIQELFKRISEQFSAMFRRKAFLHWYTGEGMDEMEFTEAESN
MNDLVSEYQQYQEATADDEFDADVDDVEHDGECV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
33 g13911.t1 CDD cd02187 beta_tubulin 2 432 0.0
32 g13911.t1 Coils Coil Coil 414 434 -
31 g13911.t1 Gene3D G3DSA:3.40.50.1440 - 1 269 6.1E-121
30 g13911.t1 Gene3D G3DSA:3.30.1330.20 - 270 379 9.6E-57
29 g13911.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 380 436 3.8E-34
3 g13911.t1 PANTHER PTHR11588 TUBULIN 1 446 0.0
4 g13911.t1 PANTHER PTHR11588:SF273 TUBULIN BETA-3 CHAIN 1 446 0.0
23 g13911.t1 PRINTS PR01161 Tubulin signature 10 30 2.6E-101
11 g13911.t1 PRINTS PR01163 Beta-tubulin signature 41 58 3.4E-116
20 g13911.t1 PRINTS PR01161 Tubulin signature 57 76 2.6E-101
14 g13911.t1 PRINTS PR01163 Beta-tubulin signature 94 105 3.4E-116
19 g13911.t1 PRINTS PR01161 Tubulin signature 99 110 2.6E-101
21 g13911.t1 PRINTS PR01161 Tubulin signature 112 136 2.6E-101
17 g13911.t1 PRINTS PR01163 Beta-tubulin signature 114 132 3.4E-116
22 g13911.t1 PRINTS PR01161 Tubulin signature 138 156 2.6E-101
24 g13911.t1 PRINTS PR01161 Tubulin signature 157 178 2.6E-101
13 g13911.t1 PRINTS PR01163 Beta-tubulin signature 158 170 3.4E-116
26 g13911.t1 PRINTS PR01161 Tubulin signature 182 195 2.6E-101
25 g13911.t1 PRINTS PR01161 Tubulin signature 196 216 2.6E-101
6 g13911.t1 PRINTS PR01163 Beta-tubulin signature 218 230 3.4E-116
9 g13911.t1 PRINTS PR01163 Beta-tubulin signature 236 245 3.4E-116
10 g13911.t1 PRINTS PR01163 Beta-tubulin signature 251 264 3.4E-116
12 g13911.t1 PRINTS PR01163 Beta-tubulin signature 271 287 3.4E-116
15 g13911.t1 PRINTS PR01163 Beta-tubulin signature 317 335 3.4E-116
16 g13911.t1 PRINTS PR01163 Beta-tubulin signature 335 349 3.4E-116
8 g13911.t1 PRINTS PR01163 Beta-tubulin signature 353 376 3.4E-116
18 g13911.t1 PRINTS PR01161 Tubulin signature 376 404 2.6E-101
5 g13911.t1 PRINTS PR01163 Beta-tubulin signature 383 394 3.4E-116
7 g13911.t1 PRINTS PR01163 Beta-tubulin signature 418 436 3.4E-116
1 g13911.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 217 3.2E-66
2 g13911.t1 Pfam PF03953 Tubulin C-terminal domain 267 388 5.2E-42
34 g13911.t1 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
35 g13911.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 146 152 -
36 g13911.t1 SMART SM00864 Tubulin_4 47 250 1.5E-66
37 g13911.t1 SMART SM00865 Tubulin_C_4 252 389 1.9E-50
27 g13911.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 249 9.42E-98
28 g13911.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 250 435 2.44E-83

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