Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin alpha-3 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_3 g2687 g2687.t3 TSS g2687.t3 19716871 19716871
chr_3 g2687 g2687.t3 isoform g2687.t3 19716922 19718655
chr_3 g2687 g2687.t3 exon g2687.t3.exon1 19716922 19716968
chr_3 g2687 g2687.t3 exon g2687.t3.exon2 19718092 19718655
chr_3 g2687 g2687.t3 cds g2687.t3.CDS1 19718206 19718655
chr_3 g2687 g2687.t3 TTS g2687.t3 19718842 19718842

Sequences

>g2687.t3 Gene=g2687 Length=611
GCTAATATATTTAATTAAATTTTATCAAGCTTTTTGTCAAGCCGAAACGTATTCACTTCC
CATTGGTTACATATGCCCCAGTCATCTCAGCTGAAAAAGCTTACCATGAACAATTGAGCG
TTGCTGAAATCACAAACGCTTGTTTCGAACCAGCCAACCAAATGGTCAAATGCGATCCAC
GTCATGGTAAATACATGGCTTGCTGCATGTTGTACAGAGGTGATGTTGTACCAAAAGATG
TCAATGCAGCCATTGCTACAATCAAGACAAAACGTACCATTCAATTTGTCGATTGGTGTC
CAACTGGTTTCAAAGTTGGTATCAATTATCAACCACCAACTGTTGTTCCAGGCGGTGATT
TGGCCAAGGTTCAACGCGCTGTTTGCATGTTGTCAAACACAACTGCCATCGCTGAAGCAT
GGGCTCGTCTTGATCATAAATTCGATTTGATGTATGCCAAGCGTGCATTCGTTCACTGGT
ATGTCGGTGAAGGTATGGAAGAAGGTGAATTCTCAGAAGCTCGTGAGGATTTGGCCGCTT
TGGAGAAAGATTATGAAGAAGTTGGCATGGACTCTGGCGAGGGAGAAGGCGAAGGCGCAG
AAGAATACTAA

>g2687.t3 Gene=g2687 Length=149
MVKCDPRHGKYMACCMLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPT
VVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEA
REDLAALEKDYEEVGMDSGEGEGEGAEEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2687.t3 Coils Coil Coil 117 137 -
13 g2687.t3 Coils Coil Coil 146 149 -
12 g2687.t3 Gene3D G3DSA:3.30.1330.20 - 1 82 2.8E-49
11 g2687.t3 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 83 136 9.8E-35
2 g2687.t3 PANTHER PTHR11588:SF390 TUBULIN ALPHA CHAIN 1 144 5.8E-102
3 g2687.t3 PANTHER PTHR11588 TUBULIN 1 144 5.8E-102
4 g2687.t3 PRINTS PR01162 Alpha-tubulin signature 20 41 3.4E-57
7 g2687.t3 PRINTS PR01162 Alpha-tubulin signature 46 59 3.4E-57
6 g2687.t3 PRINTS PR01162 Alpha-tubulin signature 59 78 3.4E-57
5 g2687.t3 PRINTS PR01162 Alpha-tubulin signature 84 100 3.4E-57
8 g2687.t3 PRINTS PR01162 Alpha-tubulin signature 121 137 3.4E-57
1 g2687.t3 Pfam PF03953 Tubulin C-terminal domain 1 91 7.3E-35
10 g2687.t3 SMART SM00865 Tubulin_C_4 1 92 5.7E-9
9 g2687.t3 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 1 136 3.97E-63

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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.

Raw TPM values