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.t4 isoform g5213.t4 7841357 7844619
chr_2 g5213 g5213.t4 exon g5213.t4.exon1 7841357 7842086
chr_2 g5213 g5213.t4 TTS g5213.t4 7841359 7841359
chr_2 g5213 g5213.t4 cds g5213.t4.CDS1 7841424 7842086
chr_2 g5213 g5213.t4 exon g5213.t4.exon2 7842179 7842365
chr_2 g5213 g5213.t4 cds g5213.t4.CDS2 7842179 7842365
chr_2 g5213 g5213.t4 exon g5213.t4.exon3 7842426 7842811
chr_2 g5213 g5213.t4 cds g5213.t4.CDS3 7842426 7842811
chr_2 g5213 g5213.t4 exon g5213.t4.exon4 7844563 7844619
chr_2 g5213 g5213.t4 cds g5213.t4.CDS4 7844563 7844619
chr_2 g5213 g5213.t4 TSS g5213.t4 7844772 7844772

Sequences

>g5213.t4 Gene=g5213 Length=1360
ATGAGAGAAATTGTTCATTTACAAGTTGGCCAATGTGGCAATCAAATTGGATCAAAGTTC
TGGGAAATCATCTCAGATGAGCACGGAATTGATCCAAATGGTCACTATCATGGTGATACT
GATCTTCAATTGGAAAGAATCAACGTCTATTACAATGAAGTTAATGGAAATCGCTATGTT
CCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTCAATCACCA
TACGGAAAACTCTTTCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTGGCAATAAT
TGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGGATGTGATT
CGTAAAGAATCAGAAGGTTGTGACTGCTTGCAAGGTTTCCAATTGACTCATTCACTTGGT
GGTGGCACAGGATCAGGAATGGGTGTCATTCCATCGCCAAAAGTATCAGACACAGTCGTT
GAGCCATACAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGATGAAACATTC
TGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAACTTTCATCACCT
TCATATGGTGACCTCAATCATTTAGTTTCGGTCACAATGTCTGGTGTAACAACTTGCTTG
CGTTTCCCTGGTCAATTAAATGCCGATTTAAGAAAACTTGCTGTCAATATGGTTCCTTTC
CCACGTCTTCATTTCTTCATGCCCGGTTTCGCGCCATTGACAGCTAAGAACAGTCAACAA
TATCGCGCTTTGACTGTTAATGAATTAACACAACAAATGTTTGATGCCAAAAATATGATG
ACAGCTTGTGATCCAAGACACGGTCGTTATTTGACTGTTGCTGCAATTTTCCGTGGTCAA
ATGTCAATGAAAGAAGTTGATGAACAAATGTTGGGTGTGCAGAATAAAAACAGCAGCTAT
TTTGTCGAGTGGATTCCAAACAATGTAAAAGTTGCTGTTTGTGATATTCCACCGAGAGGT
CTTCGTATGGCAGCAACATTCATTGGAAACACAACAGCAATTCAAGAAATTTTCAAGCGA
ATTTCTGAGCAATTTACAGCAATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACACAGGT
GAAGGAATGGATGAAATGGAATTCACTGAAGCTGAGAGCAACATGAATGACTTGGTATCA
GAATATCAACAATATCAAGAAGCTACAGCAGAAGATGATGTTGAATATGATGATCAGGGT
GAAGTCATCGAAGAAGAAGGACCACAAGAATAAAGAAAATTATTTTGTATCAAAAAAATA
TTATTGTAATAAAGTTAAGACAATTTAGTCACTTTCATAA

>g5213.t4 Gene=g5213 Length=430
MREIVHLQVGQCGNQIGSKFWEIISDEHGIDPNGHYHGDTDLQLERINVYYNEVNGNRYV
PRSVLVDLEPGTMDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVI
RKESEGCDCLQGFQLTHSLGGGTGSGMGVIPSPKVSDTVVEPYNATLSVHQLVENTDETF
CIDNEALYDICFRTLKLSSPSYGDLNHLVSVTMSGVTTCLRFPGQLNADLRKLAVNMVPF
PRLHFFMPGFAPLTAKNSQQYRALTVNELTQQMFDAKNMMTACDPRHGRYLTVAAIFRGQ
MSMKEVDEQMLGVQNKNSSYFVEWIPNNVKVAVCDIPPRGLRMAATFIGNTTAIQEIFKR
ISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQEATAEDDVEYDDQG
EVIEEEGPQE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
29 g5213.t4 CDD cd02187 beta_tubulin 2 406 0.0
28 g5213.t4 Coils Coil Coil 388 408 -
27 g5213.t4 Gene3D G3DSA:3.40.50.1440 - 1 243 5.9E-111
26 g5213.t4 Gene3D G3DSA:3.30.1330.20 - 244 353 2.7E-55
25 g5213.t4 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 354 425 1.7E-34
34 g5213.t4 MobiDBLite mobidb-lite consensus disorder prediction 409 430 -
5 g5213.t4 PANTHER PTHR11588:SF314 TUBULIN BETA-2 CHAIN 1 149 2.6E-271
7 g5213.t4 PANTHER PTHR11588 TUBULIN 1 149 2.6E-271
4 g5213.t4 PANTHER PTHR11588:SF314 TUBULIN BETA-2 CHAIN 149 421 2.6E-271
6 g5213.t4 PANTHER PTHR11588 TUBULIN 149 421 2.6E-271
21 g5213.t4 PRINTS PR01161 Tubulin signature 10 30 2.0E-69
12 g5213.t4 PRINTS PR01163 Beta-tubulin signature 41 58 6.3E-82
22 g5213.t4 PRINTS PR01161 Tubulin signature 51 70 2.0E-69
20 g5213.t4 PRINTS PR01161 Tubulin signature 93 104 2.0E-69
19 g5213.t4 PRINTS PR01161 Tubulin signature 106 130 2.0E-69
18 g5213.t4 PRINTS PR01161 Tubulin signature 132 150 2.0E-69
13 g5213.t4 PRINTS PR01163 Beta-tubulin signature 210 219 6.3E-82
16 g5213.t4 PRINTS PR01163 Beta-tubulin signature 225 238 6.3E-82
10 g5213.t4 PRINTS PR01163 Beta-tubulin signature 245 261 6.3E-82
8 g5213.t4 PRINTS PR01163 Beta-tubulin signature 291 309 6.3E-82
11 g5213.t4 PRINTS PR01163 Beta-tubulin signature 309 323 6.3E-82
14 g5213.t4 PRINTS PR01163 Beta-tubulin signature 327 350 6.3E-82
17 g5213.t4 PRINTS PR01161 Tubulin signature 350 378 2.0E-69
15 g5213.t4 PRINTS PR01163 Beta-tubulin signature 357 368 6.3E-82
9 g5213.t4 PRINTS PR01163 Beta-tubulin signature 392 410 6.3E-82
1 g5213.t4 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 148 8.8E-48
2 g5213.t4 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 149 191 1.4E-8
3 g5213.t4 Pfam PF03953 Tubulin C-terminal domain 241 362 9.9E-43
32 g5213.t4 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
33 g5213.t4 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
30 g5213.t4 SMART SM00864 Tubulin_4 47 224 1.7E-51
31 g5213.t4 SMART SM00865 Tubulin_C_4 226 363 1.6E-47
23 g5213.t4 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 223 1.44E-91
24 g5213.t4 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 224 409 7.32E-83

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5213/g5213.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5213.t4.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