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.t8 isoform g5213.t8 7841357 7844619
chr_2 g5213 g5213.t8 exon g5213.t8.exon1 7841357 7841683
chr_2 g5213 g5213.t8 TTS g5213.t8 7841359 7841359
chr_2 g5213 g5213.t8 cds g5213.t8.CDS1 7841424 7841683
chr_2 g5213 g5213.t8 exon g5213.t8.exon2 7841870 7842086
chr_2 g5213 g5213.t8 cds g5213.t8.CDS2 7841870 7842086
chr_2 g5213 g5213.t8 exon g5213.t8.exon3 7842179 7842811
chr_2 g5213 g5213.t8 cds g5213.t8.CDS3 7842179 7842811
chr_2 g5213 g5213.t8 exon g5213.t8.exon4 7844563 7844619
chr_2 g5213 g5213.t8 cds g5213.t8.CDS4 7844563 7844619
chr_2 g5213 g5213.t8 TSS g5213.t8 7844772 7844772

Sequences

>g5213.t8 Gene=g5213 Length=1234
ATGAGAGAAATTGTTCATTTACAAGTTGGCCAATGTGGCAATCAAATTGGATCAAAGTTC
TGGGAAATCATCTCAGATGAGCACGGAATTGATCCAAATGGTCACTATCATGGTGATACT
GATCTTCAATTGGAAAGAATCAACGTCTATTACAATGAAGTTAATGGAAATCGCTATGTT
CCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTCAATCACCA
TACGGAAAACTCTTTCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTGGCAATAAT
TGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGGATGTGATT
CGTAAAGAATCAGAAGGTTGTGACTGCTTGCAAGGTTTCCAATTGACTCATTCACTTGGT
GGTGGCACAGGATCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAGAATATCCA
GATCGTATTTTGAGTACATTCAGTGTCATTCCATCGCCAAAAGTATCAGACACAGTCGTT
GAGCCATACAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGATGAAACATTC
TGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAACTTTCATCACCT
TCATATGGTGACCTCAATCATTTAGTTTCGGTCACAATGTCTGGTGTAACAACTTGCTTG
CGTTTCCCTGGTCAATTAAATGCCGATTTAAGAAAACTTGCTGTCAATATGGTTCCTTTC
CCACGTCTTCATTTCTTCATGCCCGGTTTCGCGCCATTGACAGCTAAGAACAGTCAACAA
TATCGCGCTTTGACTGTTAATGAATTAACACAACAAATGTTTGATGCCAAAAATATGATG
ACAGCTTCAACATTCATTGGAAACACAACAGCAATTCAAGAAATTTTCAAGCGAATTTCT
GAGCAATTTACAGCAATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACACAGGTGAAGGA
ATGGATGAAATGGAATTCACTGAAGCTGAGAGCAACATGAATGACTTGGTATCAGAATAT
CAACAATATCAAGAAGCTACAGCAGAAGATGATGTTGAATATGATGATCAGGGTGAAGTC
ATCGAAGAAGAAGGACCACAAGAATAAAGAAAATTATTTTGTATCAAAAAAATATTATTG
TAATAAAGTTAAGACAATTTAGTCACTTTCATAA

>g5213.t8 Gene=g5213 Length=388
MREIVHLQVGQCGNQIGSKFWEIISDEHGIDPNGHYHGDTDLQLERINVYYNEVNGNRYV
PRSVLVDLEPGTMDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVI
RKESEGCDCLQGFQLTHSLGGGTGSGMGTLLIAKIREEYPDRILSTFSVIPSPKVSDTVV
EPYNATLSVHQLVENTDETFCIDNEALYDICFRTLKLSSPSYGDLNHLVSVTMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTAKNSQQYRALTVNELTQQMFDAKNMM
TASTFIGNTTAIQEIFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEY
QQYQEATAEDDVEYDDQGEVIEEEGPQE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
29 g5213.t8 CDD cd02187 beta_tubulin 2 364 0.0
28 g5213.t8 Coils Coil Coil 346 366 -
27 g5213.t8 Gene3D G3DSA:3.40.50.1440 - 1 263 2.3E-126
26 g5213.t8 Gene3D G3DSA:3.30.1330.20 - 264 312 1.4E-15
25 g5213.t8 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 313 383 1.4E-34
34 g5213.t8 MobiDBLite mobidb-lite consensus disorder prediction 366 388 -
4 g5213.t8 PANTHER PTHR11588:SF314 TUBULIN BETA-2 CHAIN 1 302 4.0E-240
6 g5213.t8 PANTHER PTHR11588 TUBULIN 1 302 4.0E-240
3 g5213.t8 PANTHER PTHR11588:SF314 TUBULIN BETA-2 CHAIN 302 379 4.0E-240
5 g5213.t8 PANTHER PTHR11588 TUBULIN 302 379 4.0E-240
15 g5213.t8 PRINTS PR01161 Tubulin signature 10 30 5.8E-87
10 g5213.t8 PRINTS PR01163 Beta-tubulin signature 41 58 1.1E-63
22 g5213.t8 PRINTS PR01161 Tubulin signature 51 70 5.8E-87
11 g5213.t8 PRINTS PR01163 Beta-tubulin signature 88 99 1.1E-63
18 g5213.t8 PRINTS PR01161 Tubulin signature 93 104 5.8E-87
19 g5213.t8 PRINTS PR01161 Tubulin signature 106 130 5.8E-87
12 g5213.t8 PRINTS PR01163 Beta-tubulin signature 108 126 1.1E-63
20 g5213.t8 PRINTS PR01161 Tubulin signature 132 150 5.8E-87
21 g5213.t8 PRINTS PR01161 Tubulin signature 151 172 5.8E-87
7 g5213.t8 PRINTS PR01163 Beta-tubulin signature 152 164 1.1E-63
17 g5213.t8 PRINTS PR01161 Tubulin signature 176 189 5.8E-87
16 g5213.t8 PRINTS PR01161 Tubulin signature 190 210 5.8E-87
14 g5213.t8 PRINTS PR01163 Beta-tubulin signature 212 224 1.1E-63
9 g5213.t8 PRINTS PR01163 Beta-tubulin signature 230 239 1.1E-63
8 g5213.t8 PRINTS PR01163 Beta-tubulin signature 245 258 1.1E-63
13 g5213.t8 PRINTS PR01163 Beta-tubulin signature 265 281 1.1E-63
1 g5213.t8 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 211 7.7E-71
2 g5213.t8 Pfam PF03953 Tubulin C-terminal domain 261 302 4.3E-11
32 g5213.t8 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
33 g5213.t8 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
30 g5213.t8 SMART SM00864 Tubulin_4 47 244 4.8E-65
31 g5213.t8 SMART SM00865 Tubulin_C_4 246 355 5.4E-4
23 g5213.t8 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 243 1.26E-102
24 g5213.t8 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 244 367 2.47E-47

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5213/g5213.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5213.t8.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