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.t6 TSS g2687.t6 19716871 19716871
chr_3 g2687 g2687.t6 isoform g2687.t6 19716989 19718655
chr_3 g2687 g2687.t6 exon g2687.t6.exon1 19716989 19716991
chr_3 g2687 g2687.t6 cds g2687.t6.CDS1 19716989 19716991
chr_3 g2687 g2687.t6 exon g2687.t6.exon2 19717306 19717867
chr_3 g2687 g2687.t6 cds g2687.t6.CDS2 19717306 19717867
chr_3 g2687 g2687.t6 exon g2687.t6.exon3 19717964 19718655
chr_3 g2687 g2687.t6 cds g2687.t6.CDS3 19717964 19718655
chr_3 g2687 g2687.t6 TTS g2687.t6 19718842 19718842

Sequences

>g2687.t6 Gene=g2687 Length=1257
ATGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGT
TGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAATGCCATCTGACAAG
ACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAACTGGTGCAGGCAAA
CACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCGATGAAGTCCGCACT
GGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGCTGCC
AACAACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCGATTTGGTTTTGGAT
CGCATCCGTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCTTAATTTTCCACTCA
TTCGGTGGCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAACGTCTCTCAGTTGAT
TATGGCAAGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCACAAGTATCTACTGCT
GTTGTTGAACCATATAACTCAATCTGCCCAACATATACCAACTTGAATCGTTTGATTGGC
CAGATTGTCTCATCGATCACCGCATCACTCCGTTTCGATGGTGCATTGAACGTCGATTTG
ACTGAATTCCAAACTAACTTGGTACCATATCCACGTATTCACTTCCCATTGGTTACATAT
GCCCCAGTCATCTCAGCTGAAAAAGCTTACCATGAACAATTGAGCGTTGCTGAAATCACA
AACGCTTGTTTCGAACCAGCCAACCAAATGGTCAAATGCGATCCACGTCATGGTAAATAC
ATGGCTTGCTGCATGTTGTACAGAGGTGATGTTGTACCAAAAGATGTCAATGCAGCCATT
GCTACAATCAAGACAAAACGTACCATTCAATTTGTCGATTGGTGTCCAACTGGTTTCAAA
GTTGGTATCAATTATCAACCACCAACTGTTGTTCCAGGCGGTGATTTGGCCAAGGTTCAA
CGCGCTGTTTGCATGTTGTCAAACACAACTGCCATCGCTGAAGCATGGGCTCGTCTTGAT
CATAAATTCGATTTGATGTATGCCAAGCGTGCATTCGTTCACTGGTATGTCGGTGAAGGT
ATGGAAGAAGGTGAATTCTCAGAAGCTCGTGAGGATTTGGCCGCTTTGGAGAAAGATTAT
GAAGAAGTTGGCATGGACTCTGGCGAGGGAGAAGGCGAAGGCGCAGAAGAATACTAA

>g2687.t6 Gene=g2687 Length=418
MRECISVHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLD
RIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFAIYPAPQVSTA
VVEPYNSICPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLVTY
APVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCMLYRGDVVPKDVNAAI
ATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLD
HKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGMDSGEGEGEGAEEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g2687.t6 CDD cd02186 alpha_tubulin 2 403 0.0
31 g2687.t6 Coils Coil Coil 386 406 -
30 g2687.t6 Gene3D G3DSA:3.40.50.1440 - 1 236 3.8E-108
29 g2687.t6 Gene3D G3DSA:3.30.1330.20 - 237 351 6.0E-68
28 g2687.t6 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 352 405 5.8E-34
3 g2687.t6 PANTHER PTHR11588:SF304 TUBULIN ALPHA CHAIN 2 189 9.5E-283
5 g2687.t6 PANTHER PTHR11588 TUBULIN 2 189 9.5E-283
4 g2687.t6 PANTHER PTHR11588:SF304 TUBULIN ALPHA CHAIN 190 413 9.5E-283
6 g2687.t6 PANTHER PTHR11588 TUBULIN 190 413 9.5E-283
21 g2687.t6 PRINTS PR01161 Tubulin signature 10 30 6.0E-79
17 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 18 33 3.3E-103
9 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 45 58 3.3E-103
20 g2687.t6 PRINTS PR01161 Tubulin signature 53 72 6.0E-79
13 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 88 101 3.3E-103
19 g2687.t6 PRINTS PR01161 Tubulin signature 95 106 6.0E-79
22 g2687.t6 PRINTS PR01161 Tubulin signature 108 132 6.0E-79
8 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 120 128 3.3E-103
24 g2687.t6 PRINTS PR01161 Tubulin signature 134 152 6.0E-79
7 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 148 160 3.3E-103
25 g2687.t6 PRINTS PR01161 Tubulin signature 153 174 6.0E-79
11 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 161 172 3.3E-103
18 g2687.t6 PRINTS PR01161 Tubulin signature 178 191 6.0E-79
10 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 289 310 3.3E-103
14 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 315 328 3.3E-103
15 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 328 347 3.3E-103
23 g2687.t6 PRINTS PR01161 Tubulin signature 348 376 6.0E-79
16 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 353 369 3.3E-103
12 g2687.t6 PRINTS PR01162 Alpha-tubulin signature 390 406 3.3E-103
1 g2687.t6 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 188 4.6E-58
2 g2687.t6 Pfam PF03953 Tubulin C-terminal domain 231 360 5.7E-53
33 g2687.t6 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 142 148 -
34 g2687.t6 SMART SM00864 Tubulin_4 49 214 4.4E-54
35 g2687.t6 SMART SM00865 Tubulin_C_4 216 361 1.2E-60
26 g2687.t6 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 212 1.31E-83
27 g2687.t6 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 214 405 1.62E-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