Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin beta-2 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 g5213 g5213.t7 isoform g5213.t7 7841357 7844619
chr_2 g5213 g5213.t7 exon g5213.t7.exon1 7841357 7841578
chr_2 g5213 g5213.t7 TTS g5213.t7 7841359 7841359
chr_2 g5213 g5213.t7 cds g5213.t7.CDS1 7841424 7841578
chr_2 g5213 g5213.t7 exon g5213.t7.exon2 7841717 7842086
chr_2 g5213 g5213.t7 cds g5213.t7.CDS2 7841717 7842086
chr_2 g5213 g5213.t7 exon g5213.t7.exon3 7842179 7842657
chr_2 g5213 g5213.t7 cds g5213.t7.CDS3 7842179 7842657
chr_2 g5213 g5213.t7 exon g5213.t7.exon4 7844563 7844619
chr_2 g5213 g5213.t7 cds g5213.t7.CDS4 7844563 7844587
chr_2 g5213 g5213.t7 TSS g5213.t7 7844772 7844772

Sequences

>g5213.t7 Gene=g5213 Length=1128
ATGAGAGAAATTGTTCATTTACAAGTTGGCCAATGTGGCAATCAAATTGGATCAAAGGCA
CAATGGACTCTGTTCGTCAATCACCATACGGAAAACTCTTTCGTCCTGACAATTTTGTGT
TTGGACAATCAGGTGCTGGCAATAATTGGGCAAAAGGTCATTATACAGAAGGAGCAGAAC
TCGTTGATGCTGTCTTGGATGTGATTCGTAAAGAATCAGAAGGTTGTGACTGCTTGCAAG
GTTTCCAATTGACTCATTCACTTGGTGGTGGCACAGGATCAGGAATGGGAACATTATTGA
TTGCCAAAATCAGGGAAGAATATCCAGATCGTATTTTGAGTACATTCAGTGTCATTCCAT
CGCCAAAAGTATCAGACACAGTCGTTGAGCCATACAATGCAACTTTGTCAGTTCACCAAC
TGGTCGAAAACACAGATGAAACATTCTGCATTGACAATGAGGCTCTATATGACATTTGCT
TCCGTACATTGAAACTTTCATCACCTTCATATGGTGACCTCAATCATTTAGTTTCGGTCA
CAATGTCTGGTGTAACAACTTGCTTGCGTTTCCCTGGTCAATTAAATGCCGATTTAAGAA
AACTTGCTGTCAATATGGTTCCTTTCCCACGTCTTCATTTCTTCATGCCCGGTTTCGCGC
CATTGACAGCTAAGAACAGTCAACAATATCGCGCTTTGACTGTTAATGAATTAACACAAC
AAATGTTTGATGCCAAAAATATGATGACAGCTTGTGATCCAAGACACGGTCGTTATTTGA
CTGTTGCTGCAATTTTCCGTGGTCAAATGTCAATGAAAGAAGTTGATGAACAAATGTTGG
GTGTGCAGAATAAAAACAGCAGCTATTTTGTCGAGTGGATTCCAAACAATGTAAAAGTTG
CTGTTTGTGAAGGAATGGATGAAATGGAATTCACTGAAGCTGAGAGCAACATGAATGACT
TGGTATCAGAATATCAACAATATCAAGAAGCTACAGCAGAAGATGATGTTGAATATGATG
ATCAGGGTGAAGTCATCGAAGAAGAAGGACCACAAGAATAAAGAAAATTATTTTGTATCA
AAAAAATATTATTGTAATAAAGTTAAGACAATTTAGTCACTTTCATAA

>g5213.t7 Gene=g5213 Length=342
MWQSNWIKGTMDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVIRK
ESEGCDCLQGFQLTHSLGGGTGSGMGTLLIAKIREEYPDRILSTFSVIPSPKVSDTVVEP
YNATLSVHQLVENTDETFCIDNEALYDICFRTLKLSSPSYGDLNHLVSVTMSGVTTCLRF
PGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTAKNSQQYRALTVNELTQQMFDAKNMMTA
CDPRHGRYLTVAAIFRGQMSMKEVDEQMLGVQNKNSSYFVEWIPNNVKVAVCEGMDEMEF
TEAESNMNDLVSEYQQYQEATAEDDVEYDDQGEVIEEEGPQE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
28 g5213.t7 CDD cd02187 beta_tubulin 9 318 0.0
27 g5213.t7 Coils Coil Coil 300 320 -
26 g5213.t7 Gene3D G3DSA:3.40.50.1440 - 7 201 1.5E-89
25 g5213.t7 Gene3D G3DSA:3.30.1330.20 - 202 308 2.5E-46
32 g5213.t7 MobiDBLite mobidb-lite consensus disorder prediction 320 342 -
4 g5213.t7 PANTHER PTHR11588:SF89 TUBULIN BETA CHAIN 8 293 2.1E-205
6 g5213.t7 PANTHER PTHR11588 TUBULIN 8 293 2.1E-205
3 g5213.t7 PANTHER PTHR11588:SF89 TUBULIN BETA CHAIN 293 331 2.1E-205
5 g5213.t7 PANTHER PTHR11588 TUBULIN 293 331 2.1E-205
15 g5213.t7 PRINTS PR01163 Beta-tubulin signature 26 37 1.2E-74
21 g5213.t7 PRINTS PR01161 Tubulin signature 31 42 4.5E-64
22 g5213.t7 PRINTS PR01161 Tubulin signature 44 68 4.5E-64
10 g5213.t7 PRINTS PR01163 Beta-tubulin signature 46 64 1.2E-74
18 g5213.t7 PRINTS PR01161 Tubulin signature 70 88 4.5E-64
20 g5213.t7 PRINTS PR01161 Tubulin signature 89 110 4.5E-64
9 g5213.t7 PRINTS PR01163 Beta-tubulin signature 90 102 1.2E-74
19 g5213.t7 PRINTS PR01161 Tubulin signature 114 127 4.5E-64
17 g5213.t7 PRINTS PR01161 Tubulin signature 128 148 4.5E-64
12 g5213.t7 PRINTS PR01163 Beta-tubulin signature 150 162 1.2E-74
8 g5213.t7 PRINTS PR01163 Beta-tubulin signature 168 177 1.2E-74
14 g5213.t7 PRINTS PR01163 Beta-tubulin signature 183 196 1.2E-74
13 g5213.t7 PRINTS PR01163 Beta-tubulin signature 203 219 1.2E-74
16 g5213.t7 PRINTS PR01163 Beta-tubulin signature 249 267 1.2E-74
11 g5213.t7 PRINTS PR01163 Beta-tubulin signature 267 281 1.2E-74
7 g5213.t7 PRINTS PR01163 Beta-tubulin signature 285 308 1.2E-74
1 g5213.t7 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 10 149 1.3E-46
2 g5213.t7 Pfam PF03953 Tubulin C-terminal domain 199 293 1.1E-33
31 g5213.t7 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 78 84 -
29 g5213.t7 SMART SM00864 Tubulin_4 3 182 1.6E-49
30 g5213.t7 SMART SM00865 Tubulin_C_4 184 309 1.8E-31
23 g5213.t7 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 9 181 5.76E-70
24 g5213.t7 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 182 321 5.19E-53

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5213/g5213.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5213.t7.fa.iupred3.txt does not exist

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