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 g13912 g13912.t5 TTS g13912.t5 33362101 33362101
chr_1 g13912 g13912.t5 isoform g13912.t5 33362708 33366435
chr_1 g13912 g13912.t5 exon g13912.t5.exon1 33362708 33363918
chr_1 g13912 g13912.t5 cds g13912.t5.CDS1 33362708 33363918
chr_1 g13912 g13912.t5 exon g13912.t5.exon2 33366379 33366435
chr_1 g13912 g13912.t5 cds g13912.t5.CDS2 33366379 33366403
chr_1 g13912 g13912.t5 TSS g13912.t5 33366633 33366633

Sequences

>g13912.t5 Gene=g13912 Length=1268
ATGCGTGAAATCGTTCATATTCAAGCTGGTCAATGCGGAAACCAAATTGGAGCAAAGAGC
GCATCAATGTCTACTATAATGAGGCATCAGGTGGCAAATACGTTCCACGTGCTGTTTTGG
TTGATTTGGAACCAGGTACTATGGATTCAGTTCGTTCTGGTCCATTTGGTCAGATTTTCC
GACCAGACAACTTTGTTTTCGGTCAATCTGGTGCTGGTAACAATTGGGCAAAGGGTCATT
ACACTGAAGGAGCCGAACTCGTAGATTCAGTTTTGGATGTTGTCCGCAAAGAAGCTGAGT
CATGCGATTGTTTACAAGGATTCCAATTGACACATTCTCTCGGAGGTGGTACAGGTTCAG
GAATGGGAACACTTTTGATTTCAAAGATTCGTGAAGAATATCCAGATCGTATTATGAACA
CCTATTCAGTGGTGCCATCACCAAAAGTATCAGACACAGTCGTTGAGCCCTACAATGCAA
CACTTTCAGTGCACCAGCTCGTCGAAAACACAGATGAAACATACTGTATTGACAATGAAG
CTCTCTATGATATCTGTTTCCGCACACTCAAACTTACCACACCAACATACGGTGATCTCA
ATCATCTCGTCTCACTTACCATGTCTGGTGTCACTACCTGCCTTCGTTTTCCTGGTCAAC
TGAACGCTGATTTGCGTAAATTGGCTGTCAACATGGTTCCATTCCCGCGTCTTCACTTCT
TCATGCCAGGTTTTGCTCCACTCACATCACGTGGCTCACAACAGTATCGTGCATTGACAG
TTCCAGAATTGACACAACAAATGTTTGATGCCAAGAATATGATGGCTGCCTGTGATCCAA
GACATGGTCGTTATCTCACAGTCGCTGCTGTTTTTCGTGGACGTATGTCAATGAAGGAAG
TCGACGAACAAATGCTTAACATTCAAAACAAGAACAGCAGTTACTTCGTCGAATGGATTC
CAAATAACGTCAAGACAGCCGTTTGTGACATTCCACCACGTGGTCTCAAAATGAGTGCTA
CATTCATCGGTAACTCAACTGCCATCCAAGAACTCTTCAAGCGCATTTCAGAACAATTCA
CTGCTATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACACTGGTGAAGGTATGGACGAAA
TGGAATTCACAGAAGCTGAAAGCAACATGAACGATCTTGTTAGCGAATACCAACAATACC
AAGAAGCAACTGCTGACGAAGATGCCGAATTCGATGAAGAACAAGAAGCTGAAGTTGATG
AAGCTTAA

>g13912.t5 Gene=g13912 Length=411
MRKPNWSKERINVYYNEASGGKYVPRAVLVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSG
AGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIR
EEYPDRIMNTYSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLK
LTTPTYGDLNHLVSLTMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSR
GSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNIQNK
NSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLH
WYTGEGMDEMEFTEAESNMNDLVSEYQQYQEATADEDAEFDEEQEAEVDEA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g13912.t5 CDD cd02187 beta_tubulin 9 390 0.0
31 g13912.t5 Coils Coil Coil 372 392 -
30 g13912.t5 Gene3D G3DSA:3.40.50.1440 - 2 227 1.1E-103
29 g13912.t5 Gene3D G3DSA:3.30.1330.20 - 228 337 6.2E-58
28 g13912.t5 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 338 409 2.4E-35
37 g13912.t5 MobiDBLite mobidb-lite consensus disorder prediction 391 411 -
36 g13912.t5 MobiDBLite mobidb-lite consensus disorder prediction 392 411 -
3 g13912.t5 PANTHER PTHR11588:SF330 TUBULIN BETA-2B CHAIN 8 404 1.7E-282
4 g13912.t5 PANTHER PTHR11588 TUBULIN 8 404 1.7E-282
17 g13912.t5 PRINTS PR01163 Beta-tubulin signature 5 22 5.4E-120
24 g13912.t5 PRINTS PR01161 Tubulin signature 15 34 1.8E-93
6 g13912.t5 PRINTS PR01163 Beta-tubulin signature 52 63 5.4E-120
20 g13912.t5 PRINTS PR01161 Tubulin signature 57 68 1.8E-93
22 g13912.t5 PRINTS PR01161 Tubulin signature 70 94 1.8E-93
5 g13912.t5 PRINTS PR01163 Beta-tubulin signature 72 90 5.4E-120
25 g13912.t5 PRINTS PR01161 Tubulin signature 96 114 1.8E-93
23 g13912.t5 PRINTS PR01161 Tubulin signature 115 136 1.8E-93
9 g13912.t5 PRINTS PR01163 Beta-tubulin signature 116 128 5.4E-120
18 g13912.t5 PRINTS PR01161 Tubulin signature 140 153 1.8E-93
21 g13912.t5 PRINTS PR01161 Tubulin signature 154 174 1.8E-93
13 g13912.t5 PRINTS PR01163 Beta-tubulin signature 176 188 5.4E-120
8 g13912.t5 PRINTS PR01163 Beta-tubulin signature 194 203 5.4E-120
15 g13912.t5 PRINTS PR01163 Beta-tubulin signature 209 222 5.4E-120
7 g13912.t5 PRINTS PR01163 Beta-tubulin signature 229 245 5.4E-120
14 g13912.t5 PRINTS PR01163 Beta-tubulin signature 275 293 5.4E-120
16 g13912.t5 PRINTS PR01163 Beta-tubulin signature 293 307 5.4E-120
12 g13912.t5 PRINTS PR01163 Beta-tubulin signature 311 334 5.4E-120
19 g13912.t5 PRINTS PR01161 Tubulin signature 334 362 1.8E-93
10 g13912.t5 PRINTS PR01163 Beta-tubulin signature 341 352 5.4E-120
11 g13912.t5 PRINTS PR01163 Beta-tubulin signature 376 394 5.4E-120
1 g13912.t5 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 9 175 1.6E-55
2 g13912.t5 Pfam PF03953 Tubulin C-terminal domain 225 346 1.1E-42
35 g13912.t5 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 104 110 -
33 g13912.t5 SMART SM00864 Tubulin_4 11 208 3.2E-69
34 g13912.t5 SMART SM00865 Tubulin_C_4 210 347 5.6E-51
26 g13912.t5 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 7 207 1.09E-83
27 g13912.t5 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 208 393 5.49E-85

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