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 g5214 g5214.t6 TTS g5214.t6 7847531 7847531
chr_2 g5214 g5214.t6 isoform g5214.t6 7848535 7851305
chr_2 g5214 g5214.t6 exon g5214.t6.exon1 7848535 7849167
chr_2 g5214 g5214.t6 cds g5214.t6.CDS1 7848535 7849167
chr_2 g5214 g5214.t6 exon g5214.t6.exon2 7851249 7851305
chr_2 g5214 g5214.t6 cds g5214.t6.CDS2 7851249 7851305
chr_2 g5214 g5214.t6 TSS g5214.t6 7851441 7851441

Sequences

>g5214.t6 Gene=g5214 Length=690
ATGAGAGAAATTGTGCATTTGCAAGTTGGTCAGTGTGGCAATCAAATTGGATCGAAATTC
TGGGAAATCATCTCAGATGAGCACGGAATTGATCCAAATGGTCACTATCATGGTGACAAT
GATTTACAATTAGAACGAATTGACGTCTATTACAATGAAGTTAATGGAAATCGTTATGTT
CCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTCAATCACCA
TACGGAAAACTCTTCCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTGGCAACAAT
TGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGGATGTGATT
CGTAAAGAGTCAGAAGGTTGTGACTGCTTGCAAGGATTCCAATTGACTCATTCACTTGGT
GGTGGCACAGGTTCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAGAATATCCA
GATCGCATCATGAACTCTTTTTCTGTTATACCATCACCGAAAGTTTCAGACACAGTCGTT
GAGCCGTATAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGACGAAACATTC
TGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAGTTGCAGTCGCCA
ACATATGGTGATCTCAATCATTTGGTTTCG

>g5214.t6 Gene=g5214 Length=230
MREIVHLQVGQCGNQIGSKFWEIISDEHGIDPNGHYHGDNDLQLERIDVYYNEVNGNRYV
PRSVLVDLEPGTMDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVI
RKESEGCDCLQGFQLTHSLGGGTGSGMGTLLIAKIREEYPDRIMNSFSVIPSPKVSDTVV
EPYNATLSVHQLVENTDETFCIDNEALYDICFRTLKLQSPTYGDLNHLVS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5214.t6 CDD cd02187 beta_tubulin 2 230 1.05616E-161
18 g5214.t6 Gene3D G3DSA:3.40.50.1440 - 1 230 6.6E-111
2 g5214.t6 PANTHER PTHR11588 TUBULIN 1 230 1.1E-149
3 g5214.t6 PANTHER PTHR11588:SF247 TUBULIN BETA-4B CHAIN 1 230 1.1E-149
9 g5214.t6 PRINTS PR01161 Tubulin signature 10 30 2.7E-88
6 g5214.t6 PRINTS PR01163 Beta-tubulin signature 41 58 3.2E-39
16 g5214.t6 PRINTS PR01161 Tubulin signature 51 70 2.7E-88
7 g5214.t6 PRINTS PR01163 Beta-tubulin signature 88 99 3.2E-39
12 g5214.t6 PRINTS PR01161 Tubulin signature 93 104 2.7E-88
13 g5214.t6 PRINTS PR01161 Tubulin signature 106 130 2.7E-88
4 g5214.t6 PRINTS PR01163 Beta-tubulin signature 108 126 3.2E-39
14 g5214.t6 PRINTS PR01161 Tubulin signature 132 150 2.7E-88
15 g5214.t6 PRINTS PR01161 Tubulin signature 151 172 2.7E-88
5 g5214.t6 PRINTS PR01163 Beta-tubulin signature 152 164 3.2E-39
11 g5214.t6 PRINTS PR01161 Tubulin signature 176 189 2.7E-88
10 g5214.t6 PRINTS PR01161 Tubulin signature 190 210 2.7E-88
8 g5214.t6 PRINTS PR01163 Beta-tubulin signature 212 224 3.2E-39
1 g5214.t6 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 211 1.4E-71
20 g5214.t6 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
21 g5214.t6 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
22 g5214.t6 SMART SM00864 Tubulin_4 47 230 2.7E-52
17 g5214.t6 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 230 5.63E-98

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5214/g5214.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5214.t6.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