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.t5 TSS g13911.t5 33336899 33336899
chr_1 g13911 g13911.t5 isoform g13911.t5 33336910 33338901
chr_1 g13911 g13911.t5 exon g13911.t5.exon1 33336910 33337018
chr_1 g13911 g13911.t5 exon g13911.t5.exon2 33337091 33338901
chr_1 g13911 g13911.t5 cds g13911.t5.CDS1 33337156 33338286
chr_1 g13911 g13911.t5 TTS g13911.t5 33338892 33338892

Sequences

>g13911.t5 Gene=g13911 Length=1920
TTTTGGGAAATTATATCTGAGGAGCATGGTATTGATGCAACCGGTATTTATAAGGGTGAA
AGTGATTTGCAATTGGAACGCGTGAGCGTTTACTATAATGAGGCATCAGCTTCGCGTTCT
TCGGGTGGCAAGTATGTGCCAAGAGCCATTCTTTTGGATCTTGAGCCTGGCACTATGGAA
GCTGTTCGTTGTGGCGCCTATGGAAAACTTTTCCGACCAGATAACTTTGTTTTCGGTCAA
TCTGGTGCTGGTAACAATTGGGCAAAGGGTCATTACACTGAAGGAGCCGAACTCGTAGAT
GCTGTTTTGGATGTTGTTCGCAAAGAGTGCGAAAATTGCGATTGTTTACAAGGATTCCAA
TTGACACATTCTCTCGGAGGTGGTACAGGTTCAGGAATGGGAACACTTTTGATTTCAAAG
ATTCGTGAAGAATATCCAGATCGTATTATGAACACCTATTCAGTTCTTCCTTCACCTAAG
GTCTCTGATACTGTCGTTGAGCCTTACAATGCAACACTCAGTATTCATCAATTGGTTGAA
AATACTGATGAAACTTATTGCATTGACAATGAAGCTCTTTATGATATTTGCTTCCGTACA
TTGAAGGTTCCTAATCCAAGTTATGGCGACCTTAATCATCTCGTCTCACTTACCATGTCT
GGTGTCACTACCTGCCTTCGTTTTCCTGGTCAACTGAACGCTGATTTGCGTAAATTGGCT
GTCAACATGGTTCCATTCCCGCGTCTTCACTTCTTCATGCCAGGTTTTGCTCCACTCACA
TCACGTGGCTCACAACAGTATCGTGCATTGACAGTTCCAGAATTGACACAACAAATGTTT
GATGCCAAGAATATGATGACAGCATGCGATCCAAGACATGGTCGTTATCTCACAGTCGCT
GCCGTTTTCCGTGGACGTATGTCAATGAAGGAAGTCGACGAACAGATGTTGGCTGTACAA
AATAAGAACAGCAGTTACTTCGTCGAATGGATTCCAAATAACGTCAAGACAGCTGTTTGT
GACATTCCACCTAAAGGATTGAAAATGTCATCGACTTTCATTGGAAACACTACTGCCATT
CAAGAACTCTTCAAGCGCATTTCAGAACAATTCTCAGCTATGTTCCGTCGTAAAGCTTTC
TTGCATTGGTACACTGGTGAAGGTATGGACGAAATGGAATTCACAGAAGCTGAAAGCAAC
ATGAACGATCTTGTTAGCGAATACCAACAATACCAAGAAGCAACTGCTGATGATGAATTC
GATGCTGATGTCGATGATGTTGAGCATGATGGCGAATGCGTGTAAACAATTTCAATTAAT
TGCCAACTTTTAACTTTTGGCGAGAGAATCGAGTGCAAAAAAAGAATTAATAATTTTTCC
CCTTTTTCATAGATTATAATTTATTGAATATCAATTTTATTCCCCTGTTTGTTTGTGAGT
AAATTTCACCTCGCTAACAATCGTTTATGCCTAAGGGGCAAATTTGAGATGATCATAAAT
ATCAATAACAATCAGCACAATGTATATTCGATAACATACATCTTTCTTTCTCTCTTGCTA
CCTCTCTAATTTAAATCCATTTCATTGCCTCGTGCTCACTTATTGACTCCCTGCCGCCAC
CATCACAGGCCTGCCTCTCGCTAAATAAGCACAATAATAAATACATACAATATAAAGTTC
AGACACTCGAAGCACGTAAGCATGTTTATCATTTCATGACACACAAGGGAGTCAACTGGC
TGGCACGAGTGAGAAGAGAGAAAGAAAGAAAAATAAATATAATGAAAAGAGTTGAGTCCT
TTAGGCAAAATTATATTATTTTATTATTGTCATTAAATCGAGTGTTTTCAAGTCTCATTT
TTCAATTTTTTTTAATTTCAAAAAATAAATAAATAACATCAAATTATATTCATTTATAAA

>g13911.t5 Gene=g13911 Length=376
MEAVRCGAYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVVRKECENCDCLQG
FQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTYSVLPSPKVSDTVVEPYNATLSIHQL
VENTDETYCIDNEALYDICFRTLKVPNPSYGDLNHLVSLTMSGVTTCLRFPGQLNADLRK
LAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMTACDPRHGRYLT
VAAVFRGRMSMKEVDEQMLAVQNKNSSYFVEWIPNNVKTAVCDIPPKGLKMSSTFIGNTT
AIQELFKRISEQFSAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQEATADD
EFDADVDDVEHDGECV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
30 g13911.t5 CDD cd02187 beta_tubulin 1 354 0.0
29 g13911.t5 Coils Coil Coil 336 356 -
28 g13911.t5 Gene3D G3DSA:3.40.50.1440 - 1 191 3.5E-87
27 g13911.t5 Gene3D G3DSA:3.30.1330.20 - 192 301 6.7E-57
26 g13911.t5 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 302 358 2.9E-34
3 g13911.t5 PANTHER PTHR11588 TUBULIN 1 368 1.7E-263
4 g13911.t5 PANTHER PTHR11588:SF273 TUBULIN BETA-3 CHAIN 1 368 1.7E-263
11 g13911.t5 PRINTS PR01163 Beta-tubulin signature 16 27 2.9E-108
18 g13911.t5 PRINTS PR01161 Tubulin signature 21 32 6.3E-80
22 g13911.t5 PRINTS PR01161 Tubulin signature 34 58 6.3E-80
6 g13911.t5 PRINTS PR01163 Beta-tubulin signature 36 54 2.9E-108
21 g13911.t5 PRINTS PR01161 Tubulin signature 60 78 6.3E-80
23 g13911.t5 PRINTS PR01161 Tubulin signature 79 100 6.3E-80
14 g13911.t5 PRINTS PR01163 Beta-tubulin signature 80 92 2.9E-108
20 g13911.t5 PRINTS PR01161 Tubulin signature 104 117 6.3E-80
17 g13911.t5 PRINTS PR01161 Tubulin signature 118 138 6.3E-80
10 g13911.t5 PRINTS PR01163 Beta-tubulin signature 140 152 2.9E-108
9 g13911.t5 PRINTS PR01163 Beta-tubulin signature 158 167 2.9E-108
8 g13911.t5 PRINTS PR01163 Beta-tubulin signature 173 186 2.9E-108
7 g13911.t5 PRINTS PR01163 Beta-tubulin signature 193 209 2.9E-108
15 g13911.t5 PRINTS PR01163 Beta-tubulin signature 239 257 2.9E-108
13 g13911.t5 PRINTS PR01163 Beta-tubulin signature 257 271 2.9E-108
12 g13911.t5 PRINTS PR01163 Beta-tubulin signature 275 298 2.9E-108
19 g13911.t5 PRINTS PR01161 Tubulin signature 298 326 6.3E-80
16 g13911.t5 PRINTS PR01163 Beta-tubulin signature 305 316 2.9E-108
5 g13911.t5 PRINTS PR01163 Beta-tubulin signature 340 358 2.9E-108
1 g13911.t5 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 8 139 1.4E-45
2 g13911.t5 Pfam PF03953 Tubulin C-terminal domain 189 310 3.6E-42
31 g13911.t5 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 68 74 -
32 g13911.t5 SMART SM00864 Tubulin_4 1 172 2.4E-48
33 g13911.t5 SMART SM00865 Tubulin_C_4 174 311 1.9E-50
24 g13911.t5 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 3 171 4.58E-69
25 g13911.t5 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 172 357 1.56E-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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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