Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin beta 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_2 g8708 g8708.t1 isoform g8708.t1 32380116 32381534
chr_2 g8708 g8708.t1 exon g8708.t1.exon1 32380116 32381423
chr_2 g8708 g8708.t1 cds g8708.t1.CDS1 32380116 32381423
chr_2 g8708 g8708.t1 exon g8708.t1.exon2 32381478 32381534
chr_2 g8708 g8708.t1 cds g8708.t1.CDS2 32381478 32381534
chr_2 g8708 g8708.t1 TSS g8708.t1 NA NA
chr_2 g8708 g8708.t1 TTS g8708.t1 NA NA

Sequences

>g8708.t1 Gene=g8708 Length=1365
ATGCGTGAAATAGTCTTCATTCAAATGGGCCAAGCTGGCAATAGAATTGGTGAGAAATTT
TGGGAAATTATTTCTGATGAGCATAATGTCAATAATTGTGGTCATTTTTATGGTCAAAGC
ATTCTGCCATATCAGCGAATTAATGTTTATTATGAATGCATTGAAAATAGTCGTTTCATG
CCTCGTTCTGTTCTTGTTGATCTTGAACCATCATATATCAACACCATTCGTGAAGGAACA
CTCGGAAAACTTTTTAATCCTGAATATATGGTCATGGGTTCAACAGGAGCTGGGAATAAT
TGGGCAAAAGGTTTTTATACAGAAGGTGCAGCTCAAATGGAAAATGTTTTAGAAATTATA
AAAAAACAAGTCGAATGTTGTGATTGTCTGCAAGGATTTCAAATGTTACATTCGATTGGT
GGTGGCACAGGAAGTGGAATGGGAAGTCTTTTACTTCGACATTTAAGAGATGACTATCAA
GATCGAATTGTTCAAACTTTCTCAGTTATTCCATCACCAAAAGTATCAGAAACTGTTGTT
GAACCTTACAATGCTGTTTTAGCATTAGCTGAATTTGCAACATGCACTGATGAGACTGTT
TGCTTTGATAATGAAGCACTTTTTGATATTTGCATAAATTCTCTTAAAATTAAATCACCA
ACAATTTATGATCTCAATCATATGGTAACAATGACAATTGCTGGTGTAACAACTTGCTTT
CGTTTCCCTGGTCAATTGAATTCTGATTTAAGAAAATTAATGACCAACATGTGTCCATTT
CCAAGACTTCACTATTTTATTTCGGGCTTTGCACCTTTACAAGCTTTGACTTTTAAAAAA
CAATATGTTAAAGTTACAGTTGATGGTTTAGCTAAAGATTTATTCAATCCATGCTTACAC
ATGGCTGGAAATAAAGAAGGTGGAAAATATCTCACTTGTGCTGCCATTTTTCGTGGATTT
TTATCATCAAAAGAAGTTGAAAGAGCAATGGTAAATGTTAGAAAATCAAATGAAAATTGT
TTTACAAAATGGATTCCAAATAGTATAAAATCAGCCATTTGTGATGTTCCACCAAGAAGT
ATGACAGCATCAGCAACTTTCTTAGCCAATACTTGCTCAATTACAAATATTTTTCAAAGA
CTCATTTGTCAATTTGATTCAATGTTTCAAAAGCGAGCTTTCATTCATTGGTATACTGGT
GAAGGCATGGAAGAGCAAGAATTTCGTGATGCAATGGAAATTGTCAATGATATTTGTGAA
GAATATCAAAATGTTTGTAATGATGAAGGCATTAGTGATGATGAATTTTCTGAAGAATCT
TTTTGTTCTGATTATGATAGTGACAGTGATGAATGTTGCTGTTAA

>g8708.t1 Gene=g8708 Length=454
MREIVFIQMGQAGNRIGEKFWEIISDEHNVNNCGHFYGQSILPYQRINVYYECIENSRFM
PRSVLVDLEPSYINTIREGTLGKLFNPEYMVMGSTGAGNNWAKGFYTEGAAQMENVLEII
KKQVECCDCLQGFQMLHSIGGGTGSGMGSLLLRHLRDDYQDRIVQTFSVIPSPKVSETVV
EPYNAVLALAEFATCTDETVCFDNEALFDICINSLKIKSPTIYDLNHMVTMTIAGVTTCF
RFPGQLNSDLRKLMTNMCPFPRLHYFISGFAPLQALTFKKQYVKVTVDGLAKDLFNPCLH
MAGNKEGGKYLTCAAIFRGFLSSKEVERAMVNVRKSNENCFTKWIPNSIKSAICDVPPRS
MTASATFLANTCSITNIFQRLICQFDSMFQKRAFIHWYTGEGMEEQEFRDAMEIVNDICE
EYQNVCNDEGISDDEFSEESFCSDYDSDSDECCC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
31 g8708.t1 CDD cd02187 beta_tubulin 2 426 0.0
30 g8708.t1 Gene3D G3DSA:3.40.50.1440 - 1 262 8.0E-104
29 g8708.t1 Gene3D G3DSA:3.30.1330.20 - 263 373 5.5E-30
28 g8708.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 374 441 4.4E-22
3 g8708.t1 PANTHER PTHR11588 TUBULIN 1 429 1.2E-181
4 g8708.t1 PANTHER PTHR11588:SF293 TUBULIN BETA CHAIN-RELATED 1 429 1.2E-181
18 g8708.t1 PRINTS PR01161 Tubulin signature 10 30 2.2E-74
9 g8708.t1 PRINTS PR01163 Beta-tubulin signature 41 58 2.4E-48
25 g8708.t1 PRINTS PR01161 Tubulin signature 51 70 2.2E-74
11 g8708.t1 PRINTS PR01163 Beta-tubulin signature 88 99 2.4E-48
21 g8708.t1 PRINTS PR01161 Tubulin signature 93 104 2.2E-74
22 g8708.t1 PRINTS PR01161 Tubulin signature 106 130 2.2E-74
13 g8708.t1 PRINTS PR01163 Beta-tubulin signature 108 126 2.4E-48
23 g8708.t1 PRINTS PR01161 Tubulin signature 132 150 2.2E-74
24 g8708.t1 PRINTS PR01161 Tubulin signature 151 172 2.2E-74
6 g8708.t1 PRINTS PR01163 Beta-tubulin signature 152 164 2.4E-48
20 g8708.t1 PRINTS PR01161 Tubulin signature 176 189 2.2E-74
19 g8708.t1 PRINTS PR01161 Tubulin signature 190 210 2.2E-74
16 g8708.t1 PRINTS PR01163 Beta-tubulin signature 212 224 2.4E-48
8 g8708.t1 PRINTS PR01163 Beta-tubulin signature 230 239 2.4E-48
7 g8708.t1 PRINTS PR01163 Beta-tubulin signature 245 258 2.4E-48
15 g8708.t1 PRINTS PR01163 Beta-tubulin signature 265 281 2.4E-48
10 g8708.t1 PRINTS PR01163 Beta-tubulin signature 311 329 2.4E-48
14 g8708.t1 PRINTS PR01163 Beta-tubulin signature 329 343 2.4E-48
5 g8708.t1 PRINTS PR01163 Beta-tubulin signature 347 370 2.4E-48
17 g8708.t1 PRINTS PR01161 Tubulin signature 370 398 2.2E-74
12 g8708.t1 PRINTS PR01163 Beta-tubulin signature 377 388 2.4E-48
1 g8708.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 211 1.1E-64
2 g8708.t1 Pfam PF03953 Tubulin C-terminal domain 261 381 1.6E-27
32 g8708.t1 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
33 g8708.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
34 g8708.t1 SMART SM00864 Tubulin_4 47 244 2.1E-49
35 g8708.t1 SMART SM00865 Tubulin_C_4 246 383 6.9E-14
26 g8708.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 243 3.53E-82
27 g8708.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 247 425 3.36E-59

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. There were no conditions that were differentially expressed