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_2 g5213 g5213.t1 TTS g5213.t1 7841359 7841359
chr_2 g5213 g5213.t1 isoform g5213.t1 7841424 7844619
chr_2 g5213 g5213.t1 exon g5213.t1.exon1 7841424 7842086
chr_2 g5213 g5213.t1 cds g5213.t1.CDS1 7841424 7842086
chr_2 g5213 g5213.t1 exon g5213.t1.exon2 7842179 7842811
chr_2 g5213 g5213.t1 cds g5213.t1.CDS2 7842179 7842811
chr_2 g5213 g5213.t1 exon g5213.t1.exon3 7844563 7844619
chr_2 g5213 g5213.t1 cds g5213.t1.CDS3 7844563 7844619
chr_2 g5213 g5213.t1 TSS g5213.t1 7844772 7844772

Sequences

>g5213.t1 Gene=g5213 Length=1353
ATGAGAGAAATTGTTCATTTACAAGTTGGCCAATGTGGCAATCAAATTGGATCAAAGTTC
TGGGAAATCATCTCAGATGAGCACGGAATTGATCCAAATGGTCACTATCATGGTGATACT
GATCTTCAATTGGAAAGAATCAACGTCTATTACAATGAAGTTAATGGAAATCGCTATGTT
CCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTCAATCACCA
TACGGAAAACTCTTTCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTGGCAATAAT
TGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGGATGTGATT
CGTAAAGAATCAGAAGGTTGTGACTGCTTGCAAGGTTTCCAATTGACTCATTCACTTGGT
GGTGGCACAGGATCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAGAATATCCA
GATCGTATTTTGAGTACATTCAGTGTCATTCCATCGCCAAAAGTATCAGACACAGTCGTT
GAGCCATACAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGATGAAACATTC
TGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAACTTTCATCACCT
TCATATGGTGACCTCAATCATTTAGTTTCGGTCACAATGTCTGGTGTAACAACTTGCTTG
CGTTTCCCTGGTCAATTAAATGCCGATTTAAGAAAACTTGCTGTCAATATGGTTCCTTTC
CCACGTCTTCATTTCTTCATGCCCGGTTTCGCGCCATTGACAGCTAAGAACAGTCAACAA
TATCGCGCTTTGACTGTTAATGAATTAACACAACAAATGTTTGATGCCAAAAATATGATG
ACAGCTTGTGATCCAAGACACGGTCGTTATTTGACTGTTGCTGCAATTTTCCGTGGTCAA
ATGTCAATGAAAGAAGTTGATGAACAAATGTTGGGTGTGCAGAATAAAAACAGCAGCTAT
TTTGTCGAGTGGATTCCAAACAATGTAAAAGTTGCTGTTTGTGATATTCCACCGAGAGGT
CTTCGTATGGCAGCAACATTCATTGGAAACACAACAGCAATTCAAGAAATTTTCAAGCGA
ATTTCTGAGCAATTTACAGCAATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACACAGGT
GAAGGAATGGATGAAATGGAATTCACTGAAGCTGAGAGCAACATGAATGACTTGGTATCA
GAATATCAACAATATCAAGAAGCTACAGCAGAAGATGATGTTGAATATGATGATCAGGGT
GAAGTCATCGAAGAAGAAGGACCACAAGAATAA

>g5213.t1 Gene=g5213 Length=450
MREIVHLQVGQCGNQIGSKFWEIISDEHGIDPNGHYHGDTDLQLERINVYYNEVNGNRYV
PRSVLVDLEPGTMDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVI
RKESEGCDCLQGFQLTHSLGGGTGSGMGTLLIAKIREEYPDRILSTFSVIPSPKVSDTVV
EPYNATLSVHQLVENTDETFCIDNEALYDICFRTLKLSSPSYGDLNHLVSVTMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTAKNSQQYRALTVNELTQQMFDAKNMM
TACDPRHGRYLTVAAIFRGQMSMKEVDEQMLGVQNKNSSYFVEWIPNNVKVAVCDIPPRG
LRMAATFIGNTTAIQEIFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQEATAEDDVEYDDQGEVIEEEGPQE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
33 g5213.t1 CDD cd02187 beta_tubulin 2 426 0.0
32 g5213.t1 Coils Coil Coil 408 428 -
31 g5213.t1 Gene3D G3DSA:3.40.50.1440 - 1 263 3.5E-126
30 g5213.t1 Gene3D G3DSA:3.30.1330.20 - 264 373 3.0E-55
29 g5213.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 374 445 1.8E-34
38 g5213.t1 MobiDBLite mobidb-lite consensus disorder prediction 429 450 -
3 g5213.t1 PANTHER PTHR11588:SF314 TUBULIN BETA-2 CHAIN 1 441 1.8E-293
4 g5213.t1 PANTHER PTHR11588 TUBULIN 1 441 1.8E-293
19 g5213.t1 PRINTS PR01161 Tubulin signature 10 30 1.3E-102
9 g5213.t1 PRINTS PR01163 Beta-tubulin signature 41 58 1.2E-115
26 g5213.t1 PRINTS PR01161 Tubulin signature 51 70 1.3E-102
11 g5213.t1 PRINTS PR01163 Beta-tubulin signature 88 99 1.2E-115
22 g5213.t1 PRINTS PR01161 Tubulin signature 93 104 1.3E-102
23 g5213.t1 PRINTS PR01161 Tubulin signature 106 130 1.3E-102
14 g5213.t1 PRINTS PR01163 Beta-tubulin signature 108 126 1.2E-115
24 g5213.t1 PRINTS PR01161 Tubulin signature 132 150 1.3E-102
25 g5213.t1 PRINTS PR01161 Tubulin signature 151 172 1.3E-102
6 g5213.t1 PRINTS PR01163 Beta-tubulin signature 152 164 1.2E-115
21 g5213.t1 PRINTS PR01161 Tubulin signature 176 189 1.3E-102
20 g5213.t1 PRINTS PR01161 Tubulin signature 190 210 1.3E-102
17 g5213.t1 PRINTS PR01163 Beta-tubulin signature 212 224 1.2E-115
8 g5213.t1 PRINTS PR01163 Beta-tubulin signature 230 239 1.2E-115
7 g5213.t1 PRINTS PR01163 Beta-tubulin signature 245 258 1.2E-115
16 g5213.t1 PRINTS PR01163 Beta-tubulin signature 265 281 1.2E-115
10 g5213.t1 PRINTS PR01163 Beta-tubulin signature 311 329 1.2E-115
15 g5213.t1 PRINTS PR01163 Beta-tubulin signature 329 343 1.2E-115
5 g5213.t1 PRINTS PR01163 Beta-tubulin signature 347 370 1.2E-115
18 g5213.t1 PRINTS PR01161 Tubulin signature 370 398 1.3E-102
13 g5213.t1 PRINTS PR01163 Beta-tubulin signature 377 388 1.2E-115
12 g5213.t1 PRINTS PR01163 Beta-tubulin signature 412 430 1.2E-115
1 g5213.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 211 1.1E-70
2 g5213.t1 Pfam PF03953 Tubulin C-terminal domain 261 382 1.1E-42
36 g5213.t1 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
37 g5213.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
34 g5213.t1 SMART SM00864 Tubulin_4 47 244 4.8E-65
35 g5213.t1 SMART SM00865 Tubulin_C_4 246 383 1.6E-47
27 g5213.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 243 1.96E-102
28 g5213.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 244 429 8.24E-83

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5213/g5213.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5213.t1.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

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