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.t3 isoform g13911.t3 33334450 33338901
chr_1 g13911 g13911.t3 exon g13911.t3.exon1 33334450 33334524
chr_1 g13911 g13911.t3 cds g13911.t3.CDS1 33334480 33334524
chr_1 g13911 g13911.t3 exon g13911.t3.exon2 33336910 33337018
chr_1 g13911 g13911.t3 cds g13911.t3.CDS2 33336910 33337018
chr_1 g13911 g13911.t3 exon g13911.t3.exon3 33337088 33338901
chr_1 g13911 g13911.t3 cds g13911.t3.CDS3 33337088 33338286
chr_1 g13911 g13911.t3 TTS g13911.t3 33338892 33338892
chr_1 g13911 g13911.t3 TSS g13911.t3 NA NA

Sequences

>g13911.t3 Gene=g13911 Length=1998
GAATAAATTTTCAACTCACTATGTTTGCGAATGACTGACTATTCATTAACTTTTCAAGTG
GAAATGAAAATTTCTTTTTGGGAAATTATATCTGAGGAGCATGGTATTGATGCAACCGGT
ATTTATAAGGGTGAAAGTGATTTGCAATTGGAACGCGTGAGCGTTTACTATAATGAGGCA
TCAGCAGCTTCGCGTTCTTCGGGTGGCAAGTATGTGCCAAGAGCCATTCTTTTGGATCTT
GAGCCTGGCACTATGGAAGCTGTTCGTTGTGGCGCCTATGGAAAACTTTTCCGACCAGAT
AACTTTGTTTTCGGTCAATCTGGTGCTGGTAACAATTGGGCAAAGGGTCATTACACTGAA
GGAGCCGAACTCGTAGATGCTGTTTTGGATGTTGTTCGCAAAGAGTGCGAAAATTGCGAT
TGTTTACAAGGATTCCAATTGACACATTCTCTCGGAGGTGGTACAGGTTCAGGAATGGGA
ACACTTTTGATTTCAAAGATTCGTGAAGAATATCCAGATCGTATTATGAACACCTATTCA
GTTCTTCCTTCACCTAAGGTCTCTGATACTGTCGTTGAGCCTTACAATGCAACACTCAGT
ATTCATCAATTGGTTGAAAATACTGATGAAACTTATTGCATTGACAATGAAGCTCTTTAT
GATATTTGCTTCCGTACATTGAAGGTTCCTAATCCAAGTTATGGCGACCTTAATCATCTC
GTCTCACTTACCATGTCTGGTGTCACTACCTGCCTTCGTTTTCCTGGTCAACTGAACGCT
GATTTGCGTAAATTGGCTGTCAACATGGTTCCATTCCCGCGTCTTCACTTCTTCATGCCA
GGTTTTGCTCCACTCACATCACGTGGCTCACAACAGTATCGTGCATTGACAGTTCCAGAA
TTGACACAACAAATGTTTGATGCCAAGAATATGATGACAGCATGCGATCCAAGACATGGT
CGTTATCTCACAGTCGCTGCCGTTTTCCGTGGACGTATGTCAATGAAGGAAGTCGACGAA
CAGATGTTGGCTGTACAAAATAAGAACAGCAGTTACTTCGTCGAATGGATTCCAAATAAC
GTCAAGACAGCTGTTTGTGACATTCCACCTAAAGGATTGAAAATGTCATCGACTTTCATT
GGAAACACTACTGCCATTCAAGAACTCTTCAAGCGCATTTCAGAACAATTCTCAGCTATG
TTCCGTCGTAAAGCTTTCTTGCATTGGTACACTGGTGAAGGTATGGACGAAATGGAATTC
ACAGAAGCTGAAAGCAACATGAACGATCTTGTTAGCGAATACCAACAATACCAAGAAGCA
ACTGCTGATGATGAATTCGATGCTGATGTCGATGATGTTGAGCATGATGGCGAATGCGTG
TAAACAATTTCAATTAATTGCCAACTTTTAACTTTTGGCGAGAGAATCGAGTGCAAAAAA
AGAATTAATAATTTTTCCCCTTTTTCATAGATTATAATTTATTGAATATCAATTTTATTC
CCCTGTTTGTTTGTGAGTAAATTTCACCTCGCTAACAATCGTTTATGCCTAAGGGGCAAA
TTTGAGATGATCATAAATATCAATAACAATCAGCACAATGTATATTCGATAACATACATC
TTTCTTTCTCTCTTGCTACCTCTCTAATTTAAATCCATTTCATTGCCTCGTGCTCACTTA
TTGACTCCCTGCCGCCACCATCACAGGCCTGCCTCTCGCTAAATAAGCACAATAATAAAT
ACATACAATATAAAGTTCAGACACTCGAAGCACGTAAGCATGTTTATCATTTCATGACAC
ACAAGGGAGTCAACTGGCTGGCACGAGTGAGAAGAGAGAAAGAAAGAAAAATAAATATAA
TGAAAAGAGTTGAGTCCTTTAGGCAAAATTATATTATTTTATTATTGTCATTAAATCGAG
TGTTTTCAAGTCTCATTTTTCAATTTTTTTTAATTTCAAAAAATAAATAAATAACATCAA
ATTATATTCATTTATAAA

>g13911.t3 Gene=g13911 Length=450
MTDYSLTFQVEMKISFWEIISEEHGIDATGIYKGESDLQLERVSVYYNEASAASRSSGGK
YVPRAILLDLEPGTMEAVRCGAYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLD
VVRKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTYSVLPSPKVSDT
VVEPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKVPNPSYGDLNHLVSLTMSGVTT
CLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKN
MMTACDPRHGRYLTVAAVFRGRMSMKEVDEQMLAVQNKNSSYFVEWIPNNVKTAVCDIPP
KGLKMSSTFIGNTTAIQELFKRISEQFSAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDL
VSEYQQYQEATADDEFDADVDDVEHDGECV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
33 g13911.t3 CDD cd02187 beta_tubulin 15 428 0.0
32 g13911.t3 Coils Coil Coil 410 430 -
31 g13911.t3 Gene3D G3DSA:3.40.50.1440 - 10 265 2.1E-107
30 g13911.t3 Gene3D G3DSA:3.30.1330.20 - 266 375 9.4E-57
29 g13911.t3 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 376 432 3.7E-34
3 g13911.t3 PANTHER PTHR11588 TUBULIN 14 442 0.0
4 g13911.t3 PANTHER PTHR11588:SF273 TUBULIN BETA-3 CHAIN 14 442 0.0
22 g13911.t3 PRINTS PR01161 Tubulin signature 6 26 2.8E-93
8 g13911.t3 PRINTS PR01163 Beta-tubulin signature 37 54 3.1E-116
21 g13911.t3 PRINTS PR01161 Tubulin signature 53 72 2.8E-93
17 g13911.t3 PRINTS PR01163 Beta-tubulin signature 90 101 3.1E-116
20 g13911.t3 PRINTS PR01161 Tubulin signature 95 106 2.8E-93
23 g13911.t3 PRINTS PR01161 Tubulin signature 108 132 2.8E-93
14 g13911.t3 PRINTS PR01163 Beta-tubulin signature 110 128 3.1E-116
25 g13911.t3 PRINTS PR01161 Tubulin signature 134 152 2.8E-93
26 g13911.t3 PRINTS PR01161 Tubulin signature 153 174 2.8E-93
13 g13911.t3 PRINTS PR01163 Beta-tubulin signature 154 166 3.1E-116
18 g13911.t3 PRINTS PR01161 Tubulin signature 178 191 2.8E-93
24 g13911.t3 PRINTS PR01161 Tubulin signature 192 212 2.8E-93
9 g13911.t3 PRINTS PR01163 Beta-tubulin signature 214 226 3.1E-116
11 g13911.t3 PRINTS PR01163 Beta-tubulin signature 232 241 3.1E-116
7 g13911.t3 PRINTS PR01163 Beta-tubulin signature 247 260 3.1E-116
15 g13911.t3 PRINTS PR01163 Beta-tubulin signature 267 283 3.1E-116
16 g13911.t3 PRINTS PR01163 Beta-tubulin signature 313 331 3.1E-116
12 g13911.t3 PRINTS PR01163 Beta-tubulin signature 331 345 3.1E-116
10 g13911.t3 PRINTS PR01163 Beta-tubulin signature 349 372 3.1E-116
19 g13911.t3 PRINTS PR01161 Tubulin signature 372 400 2.8E-93
6 g13911.t3 PRINTS PR01163 Beta-tubulin signature 379 390 3.1E-116
5 g13911.t3 PRINTS PR01163 Beta-tubulin signature 414 432 3.1E-116
1 g13911.t3 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 15 213 9.3E-57
2 g13911.t3 Pfam PF03953 Tubulin C-terminal domain 263 384 5.1E-42
34 g13911.t3 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 142 148 -
35 g13911.t3 SMART SM00864 Tubulin_4 43 246 1.5E-66
36 g13911.t3 SMART SM00865 Tubulin_C_4 248 385 1.9E-50
27 g13911.t3 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 15 245 4.97E-86
28 g13911.t3 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 246 431 2.41E-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