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.t3 isoform g5213.t3 7841357 7842696
chr_2 g5213 g5213.t3 exon g5213.t3.exon1 7841357 7842086
chr_2 g5213 g5213.t3 TTS g5213.t3 7841359 7841359
chr_2 g5213 g5213.t3 cds g5213.t3.CDS1 7841424 7842086
chr_2 g5213 g5213.t3 exon g5213.t3.exon2 7842179 7842696
chr_2 g5213 g5213.t3 cds g5213.t3.CDS2 7842179 7842652
chr_2 g5213 g5213.t3 TSS g5213.t3 NA NA

Sequences

>g5213.t3 Gene=g5213 Length=1248
GCTATGTTCCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTC
AATCACCATACGGAAAACTCTTTCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTG
GCAATAATTGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGG
ATGTGATTCGTAAAGAATCAGAAGGTTGTGACTGCTTGCAAGGTTTCCAATTGACTCATT
CACTTGGTGGTGGCACAGGATCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAG
AATATCCAGATCGTATTTTGAGTACATTCAGTGTCATTCCATCGCCAAAAGTATCAGACA
CAGTCGTTGAGCCATACAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGATG
AAACATTCTGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAACTTT
CATCACCTTCATATGGTGACCTCAATCATTTAGTTTCGGTCACAATGTCTGGTGTAACAA
CTTGCTTGCGTTTCCCTGGTCAATTAAATGCCGATTTAAGAAAACTTGCTGTCAATATGG
TTCCTTTCCCACGTCTTCATTTCTTCATGCCCGGTTTCGCGCCATTGACAGCTAAGAACA
GTCAACAATATCGCGCTTTGACTGTTAATGAATTAACACAACAAATGTTTGATGCCAAAA
ATATGATGACAGCTTGTGATCCAAGACACGGTCGTTATTTGACTGTTGCTGCAATTTTCC
GTGGTCAAATGTCAATGAAAGAAGTTGATGAACAAATGTTGGGTGTGCAGAATAAAAACA
GCAGCTATTTTGTCGAGTGGATTCCAAACAATGTAAAAGTTGCTGTTTGTGATATTCCAC
CGAGAGGTCTTCGTATGGCAGCAACATTCATTGGAAACACAACAGCAATTCAAGAAATTT
TCAAGCGAATTTCTGAGCAATTTACAGCAATGTTCCGTCGTAAAGCTTTCTTGCATTGGT
ACACAGGTGAAGGAATGGATGAAATGGAATTCACTGAAGCTGAGAGCAACATGAATGACT
TGGTATCAGAATATCAACAATATCAAGAAGCTACAGCAGAAGATGATGTTGAATATGATG
ATCAGGGTGAAGTCATCGAAGAAGAAGGACCACAAGAATAAAGAAAATTATTTTGTATCA
AAAAAATATTATTGTAATAAAGTTAAGACAATTTAGTCACTTTCATAA

>g5213.t3 Gene=g5213 Length=378
MDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVIRKESEGCDCLQG
FQLTHSLGGGTGSGMGTLLIAKIREEYPDRILSTFSVIPSPKVSDTVVEPYNATLSVHQL
VENTDETFCIDNEALYDICFRTLKLSSPSYGDLNHLVSVTMSGVTTCLRFPGQLNADLRK
LAVNMVPFPRLHFFMPGFAPLTAKNSQQYRALTVNELTQQMFDAKNMMTACDPRHGRYLT
VAAIFRGQMSMKEVDEQMLGVQNKNSSYFVEWIPNNVKVAVCDIPPRGLRMAATFIGNTT
AIQEIFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQEATAED
DVEYDDQGEVIEEEGPQE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
30 g5213.t3 CDD cd02187 beta_tubulin 1 354 0.0
29 g5213.t3 Coils Coil Coil 336 356 -
28 g5213.t3 Gene3D G3DSA:3.40.50.1440 - 1 191 2.1E-88
27 g5213.t3 Gene3D G3DSA:3.30.1330.20 - 192 301 2.1E-55
26 g5213.t3 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 302 373 1.4E-34
34 g5213.t3 MobiDBLite mobidb-lite consensus disorder prediction 357 378 -
3 g5213.t3 PANTHER PTHR11588:SF89 TUBULIN BETA CHAIN 1 367 9.0E-248
4 g5213.t3 PANTHER PTHR11588 TUBULIN 1 367 9.0E-248
11 g5213.t3 PRINTS PR01163 Beta-tubulin signature 16 27 2.3E-106
18 g5213.t3 PRINTS PR01161 Tubulin signature 21 32 6.1E-80
22 g5213.t3 PRINTS PR01161 Tubulin signature 34 58 6.1E-80
6 g5213.t3 PRINTS PR01163 Beta-tubulin signature 36 54 2.3E-106
21 g5213.t3 PRINTS PR01161 Tubulin signature 60 78 6.1E-80
23 g5213.t3 PRINTS PR01161 Tubulin signature 79 100 6.1E-80
14 g5213.t3 PRINTS PR01163 Beta-tubulin signature 80 92 2.3E-106
20 g5213.t3 PRINTS PR01161 Tubulin signature 104 117 6.1E-80
17 g5213.t3 PRINTS PR01161 Tubulin signature 118 138 6.1E-80
10 g5213.t3 PRINTS PR01163 Beta-tubulin signature 140 152 2.3E-106
9 g5213.t3 PRINTS PR01163 Beta-tubulin signature 158 167 2.3E-106
8 g5213.t3 PRINTS PR01163 Beta-tubulin signature 173 186 2.3E-106
7 g5213.t3 PRINTS PR01163 Beta-tubulin signature 193 209 2.3E-106
15 g5213.t3 PRINTS PR01163 Beta-tubulin signature 239 257 2.3E-106
13 g5213.t3 PRINTS PR01163 Beta-tubulin signature 257 271 2.3E-106
12 g5213.t3 PRINTS PR01163 Beta-tubulin signature 275 298 2.3E-106
19 g5213.t3 PRINTS PR01161 Tubulin signature 298 326 6.1E-80
16 g5213.t3 PRINTS PR01163 Beta-tubulin signature 305 316 2.3E-106
5 g5213.t3 PRINTS PR01163 Beta-tubulin signature 340 358 2.3E-106
1 g5213.t3 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 4 139 3.5E-46
2 g5213.t3 Pfam PF03953 Tubulin C-terminal domain 189 310 7.7E-43
33 g5213.t3 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 68 74 -
31 g5213.t3 SMART SM00864 Tubulin_4 1 172 4.7E-47
32 g5213.t3 SMART SM00865 Tubulin_C_4 174 311 1.6E-47
24 g5213.t3 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 171 4.19E-69
25 g5213.t3 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 172 357 5.49E-83

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5213/g5213.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5213.t3.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.

Raw TPM values