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.t4 TTS g5214.t4 7847531 7847531
chr_2 g5214 g5214.t4 isoform g5214.t4 7847807 7848808
chr_2 g5214 g5214.t4 exon g5214.t4.exon1 7847807 7848469
chr_2 g5214 g5214.t4 cds g5214.t4.CDS1 7847807 7848469
chr_2 g5214 g5214.t4 exon g5214.t4.exon2 7848535 7848808
chr_2 g5214 g5214.t4 cds g5214.t4.CDS2 7848535 7848786
chr_2 g5214 g5214.t4 TSS g5214.t4 NA NA

Sequences

>g5214.t4 Gene=g5214 Length=937
TGGTGGTGGCACAGGTTCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAGAATA
TCCAGATCGCATCATGAACTCTTTTTCTGTTATACCATCACCGAAAGTTTCAGACACAGT
CGTTGAGCCGTATAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGACGAAAC
ATTCTGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAGTTGCAGTC
GCCAACATATGGTGATCTCAATCATTTGGTTTCGATTACCATGTCAGGTGTAACAACTTG
CTTGCGTTTTCCTGGTCAATTAAATGCTGATTTGAGAAAACTTGCTGTCAATATGGTTCC
TTTCCCGCGTCTTCACTTTTTTATGCCGGGTTTCGCGCCATTGACAGCTAAGAACAGTCA
ACAATATCGCGCACTTAGCGTTGCTGATTTGACTCAACAAATGTTTGATGCCAAAAATAT
GATGACAGCTTGTGATCCAAGACATGGTCGTTATTTGACTGTTGCTGCAATTTTCCGTGG
TCAAATGTCAATGAAAGAAGTTGATGAACAAATGTTGGGTGTGCAGAACAAGAACAGCAG
CTATTTTGTCGAGTGGATTCCAAACAATGTAAAAGTTGCTGTTTGTGATATTCCACCGAG
AGGATTAAAAATGGCAGCAACATTTATTGGCAATTCTACAGCAATTCAAGAAATTTTCAA
GCGAATTTCTGAGCAATTTACAGCAATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACAC
AGGTGAAGGAATGGATGAAATGGAATTCACTGAAGCTGAGAGTAACATGAATGACTTGGT
ATCAGAATATCAACAATATCAAGAAGCATCAGCTGATGATGACATTGAATTTGACGAAAA
TGAAGAAATTGAGCAAAATCCAAATGAAGCTTGTTAA

>g5214.t4 Gene=g5214 Length=304
MGTLLIAKIREEYPDRIMNSFSVIPSPKVSDTVVEPYNATLSVHQLVENTDETFCIDNEA
LYDICFRTLKLQSPTYGDLNHLVSITMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFF
MPGFAPLTAKNSQQYRALSVADLTQQMFDAKNMMTACDPRHGRYLTVAAIFRGQMSMKEV
DEQMLGVQNKNSSYFVEWIPNNVKVAVCDIPPRGLKMAATFIGNSTAIQEIFKRISEQFT
AMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQEASADDDIEFDENEEIEQNP
NEAC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g5214.t4 CDD cd02187 beta_tubulin 1 280 0.0
24 g5214.t4 Coils Coil Coil 262 282 -
23 g5214.t4 Gene3D G3DSA:3.40.50.1440 - 1 117 1.7E-45
22 g5214.t4 Gene3D G3DSA:3.30.1330.20 - 118 227 6.4E-56
21 g5214.t4 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 228 299 1.3E-34
27 g5214.t4 MobiDBLite mobidb-lite consensus disorder prediction 283 304 -
3 g5214.t4 PANTHER PTHR11588:SF89 TUBULIN BETA CHAIN 1 294 4.4E-198
4 g5214.t4 PANTHER PTHR11588 TUBULIN 1 294 4.4E-198
15 g5214.t4 PRINTS PR01161 Tubulin signature 5 26 5.0E-43
12 g5214.t4 PRINTS PR01163 Beta-tubulin signature 6 18 4.0E-88
17 g5214.t4 PRINTS PR01161 Tubulin signature 30 43 5.0E-43
16 g5214.t4 PRINTS PR01161 Tubulin signature 44 64 5.0E-43
8 g5214.t4 PRINTS PR01163 Beta-tubulin signature 66 78 4.0E-88
9 g5214.t4 PRINTS PR01163 Beta-tubulin signature 84 93 4.0E-88
10 g5214.t4 PRINTS PR01163 Beta-tubulin signature 99 112 4.0E-88
13 g5214.t4 PRINTS PR01163 Beta-tubulin signature 119 135 4.0E-88
6 g5214.t4 PRINTS PR01163 Beta-tubulin signature 165 183 4.0E-88
5 g5214.t4 PRINTS PR01163 Beta-tubulin signature 183 197 4.0E-88
14 g5214.t4 PRINTS PR01163 Beta-tubulin signature 201 224 4.0E-88
18 g5214.t4 PRINTS PR01161 Tubulin signature 224 252 5.0E-43
7 g5214.t4 PRINTS PR01163 Beta-tubulin signature 231 242 4.0E-88
11 g5214.t4 PRINTS PR01163 Beta-tubulin signature 266 284 4.0E-88
1 g5214.t4 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 2 65 2.9E-15
2 g5214.t4 Pfam PF03953 Tubulin C-terminal domain 115 236 2.8E-43
26 g5214.t4 SMART SM00865 Tubulin_C_4 100 237 2.7E-49
19 g5214.t4 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 97 1.57E-32
20 g5214.t4 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 98 282 9.46E-84

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5214/g5214.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5214.t4.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