Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin alpha-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_3 g2687 g2687.t11 TSS g2687.t11 19716871 19716871
chr_3 g2687 g2687.t11 isoform g2687.t11 19716989 19718655
chr_3 g2687 g2687.t11 exon g2687.t11.exon1 19716989 19716991
chr_3 g2687 g2687.t11 exon g2687.t11.exon2 19717306 19717375
chr_3 g2687 g2687.t11 cds g2687.t11.CDS1 19717311 19717375
chr_3 g2687 g2687.t11 exon g2687.t11.exon3 19717563 19718655
chr_3 g2687 g2687.t11 cds g2687.t11.CDS2 19717563 19718655
chr_3 g2687 g2687.t11 TTS g2687.t11 19718842 19718842

Sequences

>g2687.t11 Gene=g2687 Length=1166
ATGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGT
TGGGAACTTTACTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGCTGCCAACAACT
ACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCGATTTGGTTTTGGATCGCATCC
GTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCTTAATTTTCCACTCATTCGGTG
GCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAACGTCTCTCAGTTGATTATGGCA
AGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCACAAGTATCTACTGCTGTTGTTG
AACCATATAACTCAATCTTGACAACACATACAACTTTGGAACACTCTGACTGCGCATTCA
TGGTCGATAACGAAGCTATCTATGACATCTGCCGTCGTAATTTGGACATTGAACGCCCAA
CATATACCAACTTGAATCGTTTGATTGGCCAGATTGTCTCATCGATCACCGCATCACTCC
GTTTCGATGGTGCATTGAACGTCGATTTGACTGAATTCCAAACTAACTTGGTACCATATC
CACGTATTCACTTCCCATTGGTTACATATGCCCCAGTCATCTCAGCTGAAAAAGCTTACC
ATGAACAATTGAGCGTTGCTGAAATCACAAACGCTTGTTTCGAACCAGCCAACCAAATGG
TCAAATGCGATCCACGTCATGGTAAATACATGGCTTGCTGCATGTTGTACAGAGGTGATG
TTGTACCAAAAGATGTCAATGCAGCCATTGCTACAATCAAGACAAAACGTACCATTCAAT
TTGTCGATTGGTGTCCAACTGGTTTCAAAGTTGGTATCAATTATCAACCACCAACTGTTG
TTCCAGGCGGTGATTTGGCCAAGGTTCAACGCGCTGTTTGCATGTTGTCAAACACAACTG
CCATCGCTGAAGCATGGGCTCGTCTTGATCATAAATTCGATTTGATGTATGCCAAGCGTG
CATTCGTTCACTGGTATGTCGGTGAAGGTATGGAAGAAGGTGAATTCTCAGAAGCTCGTG
AGGATTTGGCCGCTTTGGAGAAAGATTATGAAGAAGTTGGCATGGACTCTGGCGAGGGAG
AAGGCGAAGGCGCAGAAGAATACTAA

>g2687.t11 Gene=g2687 Length=385
MYLSSCWSSWCPNRKCLLGTLLHPEQLITGKEDAANNYARGHYTIGKEIVDLVLDRIRKL
ADQCTGLQGFLIFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFAIYPAPQVSTAVVEPY
NSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFD
GALNVDLTEFQTNLVPYPRIHFPLVTYAPVISAEKAYHEQLSVAEITNACFEPANQMVKC
DPRHGKYMACCMLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPG
GDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDL
AALEKDYEEVGMDSGEGEGEGAEEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
29 g2687.t11 CDD cd02186 alpha_tubulin 14 370 0.0
28 g2687.t11 Coils Coil Coil 353 373 -
27 g2687.t11 Gene3D G3DSA:3.40.50.1440 - 12 203 2.1E-86
26 g2687.t11 Gene3D G3DSA:3.30.1330.20 - 204 318 5.1E-68
25 g2687.t11 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 319 372 5.1E-34
3 g2687.t11 PANTHER PTHR11588:SF366 TUBULIN ALPHA-3 CHAIN 20 382 1.5E-260
4 g2687.t11 PANTHER PTHR11588 TUBULIN 20 382 1.5E-260
8 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 23 36 3.0E-102
17 g2687.t11 PRINTS PR01161 Tubulin signature 30 41 4.7E-68
18 g2687.t11 PRINTS PR01161 Tubulin signature 43 67 4.7E-68
15 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 55 63 3.0E-102
21 g2687.t11 PRINTS PR01161 Tubulin signature 69 87 4.7E-68
12 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 83 95 3.0E-102
16 g2687.t11 PRINTS PR01161 Tubulin signature 88 109 4.7E-68
9 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 96 107 3.0E-102
20 g2687.t11 PRINTS PR01161 Tubulin signature 113 126 4.7E-68
19 g2687.t11 PRINTS PR01161 Tubulin signature 127 147 4.7E-68
10 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 149 161 3.0E-102
13 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 209 224 3.0E-102
7 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 256 277 3.0E-102
5 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 282 295 3.0E-102
11 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 295 314 3.0E-102
22 g2687.t11 PRINTS PR01161 Tubulin signature 315 343 4.7E-68
14 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 320 336 3.0E-102
6 g2687.t11 PRINTS PR01162 Alpha-tubulin signature 357 373 3.0E-102
1 g2687.t11 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 20 148 8.5E-41
2 g2687.t11 Pfam PF03953 Tubulin C-terminal domain 198 327 4.9E-53
30 g2687.t11 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 77 83 -
31 g2687.t11 SMART SM00864 Tubulin_4 15 181 5.9E-53
32 g2687.t11 SMART SM00865 Tubulin_C_4 183 328 1.2E-60
23 g2687.t11 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 17 179 1.28E-64
24 g2687.t11 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 181 372 1.31E-87

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
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