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 g5213 g5213.t5 isoform g5213.t5 7841357 7844619
chr_2 g5213 g5213.t5 exon g5213.t5.exon1 7841357 7841953
chr_2 g5213 g5213.t5 TTS g5213.t5 7841359 7841359
chr_2 g5213 g5213.t5 cds g5213.t5.CDS1 7841424 7841900
chr_2 g5213 g5213.t5 exon g5213.t5.exon2 7842254 7842811
chr_2 g5213 g5213.t5 exon g5213.t5.exon3 7844563 7844619
chr_2 g5213 g5213.t5 TSS g5213.t5 7844772 7844772

Sequences

>g5213.t5 Gene=g5213 Length=1212
ATGAGAGAAATTGTTCATTTACAAGTTGGCCAATGTGGCAATCAAATTGGATCAAAGTTC
TGGGAAATCATCTCAGATGAGCACGGAATTGATCCAAATGGTCACTATCATGGTGATACT
GATCTTCAATTGGAAAGAATCAACGTCTATTACAATGAAGTTAATGGAAATCGCTATGTT
CCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTCAATCACCA
TACGGAAAACTCTTTCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTGGCAATAAT
TGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGGATGTGATT
CGTAAAGAATCAGAAGGTTGTGACTGCTTGCAAGGTTTCCAATTGACTCATTCACTTGGT
GGTGGCACAGGATCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAGAATATCCA
GATCGTATTTTGAGTACATTCAGTGTCATTCCATCGCCAAAAGTATCAGACACAGTCGTT
GAGCCATACAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGATGAAACATTC
TGCATTGACAATGAGCTAAGAACAGTCAACAATATCGCGCTTTGACTGTTAATGAATTAA
CACAACAAATGTTTGATGCCAAAAATATGATGACAGCTTGTGATCCAAGACACGGTCGTT
ATTTGACTGTTGCTGCAATTTTCCGTGGTCAAATGTCAATGAAAGAAGTTGATGAACAAA
TGTTGGGTGTGCAGAATAAAAACAGCAGCTATTTTGTCGAGTGGATTCCAAACAATGTAA
AAGTTGCTGTTTGTGATATTCCACCGAGAGGTCTTCGTATGGCAGCAACATTCATTGGAA
ACACAACAGCAATTCAAGAAATTTTCAAGCGAATTTCTGAGCAATTTACAGCAATGTTCC
GTCGTAAAGCTTTCTTGCATTGGTACACAGGTGAAGGAATGGATGAAATGGAATTCACTG
AAGCTGAGAGCAACATGAATGACTTGGTATCAGAATATCAACAATATCAAGAAGCTACAG
CAGAAGATGATGTTGAATATGATGATCAGGGTGAAGTCATCGAAGAAGAAGGACCACAAG
AATAAAGAAAATTATTTTGTATCAAAAAAATATTATTGTAATAAAGTTAAGACAATTTAG
TCACTTTCATAA

>g5213.t5 Gene=g5213 Length=158
MFDAKNMMTACDPRHGRYLTVAAIFRGQMSMKEVDEQMLGVQNKNSSYFVEWIPNNVKVA
VCDIPPRGLRMAATFIGNTTAIQEIFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAE
SNMNDLVSEYQQYQEATAEDDVEYDDQGEVIEEEGPQE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5213.t5 Coils Coil Coil 116 136 -
11 g5213.t5 Gene3D G3DSA:3.30.1330.20 - 1 81 1.1E-38
10 g5213.t5 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 82 153 2.6E-35
14 g5213.t5 MobiDBLite mobidb-lite consensus disorder prediction 137 158 -
2 g5213.t5 PANTHER PTHR11588:SF61 TUBULIN BETA CHAIN 2 145 7.6E-93
3 g5213.t5 PANTHER PTHR11588 TUBULIN 2 145 7.6E-93
5 g5213.t5 PRINTS PR01163 Beta-tubulin signature 19 37 1.2E-48
4 g5213.t5 PRINTS PR01163 Beta-tubulin signature 37 51 1.2E-48
7 g5213.t5 PRINTS PR01163 Beta-tubulin signature 55 78 1.2E-48
6 g5213.t5 PRINTS PR01163 Beta-tubulin signature 85 96 1.2E-48
8 g5213.t5 PRINTS PR01163 Beta-tubulin signature 120 138 1.2E-48
1 g5213.t5 Pfam PF03953 Tubulin C-terminal domain 1 90 3.9E-29
13 g5213.t5 SMART SM00865 Tubulin_C_4 1 91 4.1E-6
9 g5213.t5 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 1 137 4.58E-61

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5213/g5213.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5213.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

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