Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin beta 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.t9 TTS g5213.t9 7841359 7841359
chr_2 g5213 g5213.t9 isoform g5213.t9 7841953 7844619
chr_2 g5213 g5213.t9 exon g5213.t9.exon1 7841953 7842086
chr_2 g5213 g5213.t9 cds g5213.t9.CDS1 7841955 7842086
chr_2 g5213 g5213.t9 exon g5213.t9.exon2 7842185 7842811
chr_2 g5213 g5213.t9 cds g5213.t9.CDS2 7842185 7842811
chr_2 g5213 g5213.t9 exon g5213.t9.exon3 7844563 7844619
chr_2 g5213 g5213.t9 cds g5213.t9.CDS3 7844563 7844619
chr_2 g5213 g5213.t9 TSS g5213.t9 7844772 7844772

Sequences

>g5213.t9 Gene=g5213 Length=818
ATGAGAGAAATTGTTCATTTACAAGTTGGCCAATGTGGCAATCAAATTGGATCAAAGTTC
TGGGAAATCATCTCAGATGAGCACGGAATTGATCCAAATGGTCACTATCATGGTGATACT
GATCTTCAATTGGAAAGAATCAACGTCTATTACAATGAAGTTAATGGAAATCGCTATGTT
CCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTCAATCACCA
TACGGAAAACTCTTTCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTGGCAATAAT
TGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGGATGTGATT
CGTAAAGAATCAGAAGGTTGTGACTGCTTGCAAGGTTTCCAATTGACTCATTCACTTGGT
GGTGGCACAGGATCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAGAATATCCA
GATCGTATTTTGAGTACATTCAGTGTCATTCCATCGCCAAAAGTATCAGACACAGTCGTT
GAGCCATACAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGATGAAACATTC
TGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAACTTTCATCACCT
TCATATGGTGACCTCAATCATTTAGTCACAATGTCTGGTGTAACAACTTGCTTGCGTTTC
CCTGGTCAATTAAATGCCGATTTAAGAAAACTTGCTGTCAATATGGTTCCTTTCCCACGT
CTTCATTTCTTCATGCCCGGTTTCGCGCCATTGACAGC

>g5213.t9 Gene=g5213 Length=272
MREIVHLQVGQCGNQIGSKFWEIISDEHGIDPNGHYHGDTDLQLERINVYYNEVNGNRYV
PRSVLVDLEPGTMDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVI
RKESEGCDCLQGFQLTHSLGGGTGSGMGTLLIAKIREEYPDRILSTFSVIPSPKVSDTVV
EPYNATLSVHQLVENTDETFCIDNEALYDICFRTLKLSSPSYGDLNHLVTMSGVTTCLRF
PGQLNADLRKLAVNMVPFPRLHFFMPGFAPLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g5213.t9 CDD cd02187 beta_tubulin 2 272 0.0
21 g5213.t9 Gene3D G3DSA:3.40.50.1440 - 1 272 6.3E-126
2 g5213.t9 PANTHER PTHR11588:SF295 TUBULIN BETA CHAIN 1 272 4.3E-178
3 g5213.t9 PANTHER PTHR11588 TUBULIN 1 272 4.3E-178
11 g5213.t9 PRINTS PR01161 Tubulin signature 10 30 5.7E-88
7 g5213.t9 PRINTS PR01163 Beta-tubulin signature 41 58 3.3E-55
18 g5213.t9 PRINTS PR01161 Tubulin signature 51 70 5.7E-88
9 g5213.t9 PRINTS PR01163 Beta-tubulin signature 88 99 3.3E-55
14 g5213.t9 PRINTS PR01161 Tubulin signature 93 104 5.7E-88
15 g5213.t9 PRINTS PR01161 Tubulin signature 106 130 5.7E-88
4 g5213.t9 PRINTS PR01163 Beta-tubulin signature 108 126 3.3E-55
16 g5213.t9 PRINTS PR01161 Tubulin signature 132 150 5.7E-88
17 g5213.t9 PRINTS PR01161 Tubulin signature 151 172 5.7E-88
5 g5213.t9 PRINTS PR01163 Beta-tubulin signature 152 164 3.3E-55
13 g5213.t9 PRINTS PR01161 Tubulin signature 176 189 5.7E-88
12 g5213.t9 PRINTS PR01161 Tubulin signature 190 210 5.7E-88
10 g5213.t9 PRINTS PR01163 Beta-tubulin signature 212 224 3.3E-55
6 g5213.t9 PRINTS PR01163 Beta-tubulin signature 243 256 3.3E-55
8 g5213.t9 PRINTS PR01163 Beta-tubulin signature 263 272 3.3E-55
1 g5213.t9 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 211 2.7E-71
23 g5213.t9 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
24 g5213.t9 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
25 g5213.t9 SMART SM00864 Tubulin_4 47 242 2.6E-63
19 g5213.t9 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 241 3.01E-100
20 g5213.t9 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 242 272 1.1E-9

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5213/g5213.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5213.t9.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