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 g5214 g5214.t5 TTS g5214.t5 7847531 7847531
chr_2 g5214 g5214.t5 isoform g5214.t5 7847807 7851305
chr_2 g5214 g5214.t5 exon g5214.t5.exon1 7847807 7848255
chr_2 g5214 g5214.t5 cds g5214.t5.CDS1 7847807 7848255
chr_2 g5214 g5214.t5 exon g5214.t5.exon2 7848558 7849167
chr_2 g5214 g5214.t5 cds g5214.t5.CDS2 7848558 7849167
chr_2 g5214 g5214.t5 exon g5214.t5.exon3 7851249 7851305
chr_2 g5214 g5214.t5 cds g5214.t5.CDS3 7851249 7851305
chr_2 g5214 g5214.t5 TSS g5214.t5 7851441 7851441

Sequences

>g5214.t5 Gene=g5214 Length=1116
ATGAGAGAAATTGTGCATTTGCAAGTTGGTCAGTGTGGCAATCAAATTGGATCGAAATTC
TGGGAAATCATCTCAGATGAGCACGGAATTGATCCAAATGGTCACTATCATGGTGACAAT
GATTTACAATTAGAACGAATTGACGTCTATTACAATGAAGTTAATGGAAATCGTTATGTT
CCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTCAATCACCA
TACGGAAAACTCTTCCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTGGCAACAAT
TGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGGATGTGATT
CGTAAAGAGTCAGAAGGTTGTGACTGCTTGCAAGGATTCCAATTGACTCATTCACTTGGT
GGTGGCACAGGTTCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAGAATATCCA
GATCGCATCATGAACTCTTTTTCTGTTATACCATCACCGAAAGTTTCAGACACAGTCGTT
GAGCCGTATAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGACGAAACATTC
TGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAGTTGCAGTCGCCA
ACATATGCTTGTGATCCAAGACATGGTCGTTATTTGACTGTTGCTGCAATTTTCCGTGGT
CAAATGTCAATGAAAGAAGTTGATGAACAAATGTTGGGTGTGCAGAACAAGAACAGCAGC
TATTTTGTCGAGTGGATTCCAAACAATGTAAAAGTTGCTGTTTGTGATATTCCACCGAGA
GGATTAAAAATGGCAGCAACATTTATTGGCAATTCTACAGCAATTCAAGAAATTTTCAAG
CGAATTTCTGAGCAATTTACAGCAATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACACA
GGTGAAGGAATGGATGAAATGGAATTCACTGAAGCTGAGAGTAACATGAATGACTTGGTA
TCAGAATATCAACAATATCAAGAAGCATCAGCTGATGATGACATTGAATTTGACGAAAAT
GAAGAAATTGAGCAAAATCCAAATGAAGCTTGTTAA

>g5214.t5 Gene=g5214 Length=371
MREIVHLQVGQCGNQIGSKFWEIISDEHGIDPNGHYHGDNDLQLERIDVYYNEVNGNRYV
PRSVLVDLEPGTMDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVI
RKESEGCDCLQGFQLTHSLGGGTGSGMGTLLIAKIREEYPDRIMNSFSVIPSPKVSDTVV
EPYNATLSVHQLVENTDETFCIDNEALYDICFRTLKLQSPTYACDPRHGRYLTVAAIFRG
QMSMKEVDEQMLGVQNKNSSYFVEWIPNNVKVAVCDIPPRGLKMAATFIGNSTAIQEIFK
RISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQEASADDDIEFDEN
EEIEQNPNEAC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
26 g5214.t5 CDD cd02187 beta_tubulin 2 347 0.0
25 g5214.t5 Coils Coil Coil 329 349 -
24 g5214.t5 Gene3D G3DSA:3.40.50.1440 - 1 222 2.2E-106
23 g5214.t5 Gene3D G3DSA:3.40.50.1440 - 223 293 4.3E-14
22 g5214.t5 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 295 366 1.8E-34
31 g5214.t5 MobiDBLite mobidb-lite consensus disorder prediction 350 371 -
4 g5214.t5 PANTHER PTHR11588:SF100 TUBULIN BETA-2A CHAIN 1 222 4.3E-232
6 g5214.t5 PANTHER PTHR11588 TUBULIN 1 222 4.3E-232
3 g5214.t5 PANTHER PTHR11588:SF100 TUBULIN BETA-2A CHAIN 223 361 4.3E-232
5 g5214.t5 PANTHER PTHR11588 TUBULIN 223 361 4.3E-232
12 g5214.t5 PRINTS PR01161 Tubulin signature 10 30 5.9E-87
9 g5214.t5 PRINTS PR01163 Beta-tubulin signature 41 58 7.5E-36
19 g5214.t5 PRINTS PR01161 Tubulin signature 51 70 5.9E-87
10 g5214.t5 PRINTS PR01163 Beta-tubulin signature 88 99 7.5E-36
15 g5214.t5 PRINTS PR01161 Tubulin signature 93 104 5.9E-87
16 g5214.t5 PRINTS PR01161 Tubulin signature 106 130 5.9E-87
7 g5214.t5 PRINTS PR01163 Beta-tubulin signature 108 126 7.5E-36
17 g5214.t5 PRINTS PR01161 Tubulin signature 132 150 5.9E-87
18 g5214.t5 PRINTS PR01161 Tubulin signature 151 172 5.9E-87
8 g5214.t5 PRINTS PR01163 Beta-tubulin signature 152 164 7.5E-36
14 g5214.t5 PRINTS PR01161 Tubulin signature 176 189 5.9E-87
13 g5214.t5 PRINTS PR01161 Tubulin signature 190 210 5.9E-87
11 g5214.t5 PRINTS PR01163 Beta-tubulin signature 212 224 7.5E-36
1 g5214.t5 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 211 6.3E-71
2 g5214.t5 Pfam PF03953 Tubulin C-terminal domain 202 303 2.4E-25
29 g5214.t5 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
30 g5214.t5 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
27 g5214.t5 SMART SM00864 Tubulin_4 47 240 1.9E-48
28 g5214.t5 SMART SM00865 Tubulin_C_4 178 304 4.0E-8
20 g5214.t5 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 223 1.57E-94
21 g5214.t5 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 202 349 1.04E-57

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5214/g5214.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5214.t5.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