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.t7 TSS g2687.t7 19716871 19716871
chr_3 g2687 g2687.t7 isoform g2687.t7 19716989 19718655
chr_3 g2687 g2687.t7 exon g2687.t7.exon1 19716989 19716991
chr_3 g2687 g2687.t7 cds g2687.t7.CDS1 19716989 19716991
chr_3 g2687 g2687.t7 exon g2687.t7.exon2 19717306 19717894
chr_3 g2687 g2687.t7 cds g2687.t7.CDS2 19717306 19717894
chr_3 g2687 g2687.t7 exon g2687.t7.exon3 19718303 19718655
chr_3 g2687 g2687.t7 cds g2687.t7.CDS3 19718303 19718655
chr_3 g2687 g2687.t7 TTS g2687.t7 19718842 19718842

Sequences

>g2687.t7 Gene=g2687 Length=945
ATGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGT
TGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAATGCCATCTGACAAG
ACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAACTGGTGCAGGCAAA
CACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCGATGAAGTCCGCACT
GGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGCTGCC
AACAACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCGATTTGGTTTTGGAT
CGCATCCGTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCTTAATTTTCCACTCA
TTCGGTGGCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAACGTCTCTCAGTTGAT
TATGGCAAGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCACAAGTATCTACTGCT
GTTGTTGAACCATATAACTCAATCTTGACAACACATACAACTTTGGAACACTCAATCAAG
ACAAAACGTACCATTCAATTTGTCGATTGGTGTCCAACTGGTTTCAAAGTTGGTATCAAT
TATCAACCACCAACTGTTGTTCCAGGCGGTGATTTGGCCAAGGTTCAACGCGCTGTTTGC
ATGTTGTCAAACACAACTGCCATCGCTGAAGCATGGGCTCGTCTTGATCATAAATTCGAT
TTGATGTATGCCAAGCGTGCATTCGTTCACTGGTATGTCGGTGAAGGTATGGAAGAAGGT
GAATTCTCAGAAGCTCGTGAGGATTTGGCCGCTTTGGAGAAAGATTATGAAGAAGTTGGC
ATGGACTCTGGCGAGGGAGAAGGCGAAGGCGCAGAAGAATACTAA

>g2687.t7 Gene=g2687 Length=314
MRECISVHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLD
RIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFAIYPAPQVSTA
VVEPYNSILTTHTTLEHSIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVC
MLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVG
MDSGEGEGEGAEEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
26 g2687.t7 CDD cd02186 alpha_tubulin 2 299 0.0
25 g2687.t7 Coils Coil Coil 282 302 -
24 g2687.t7 Gene3D G3DSA:3.40.50.1440 - 1 197 6.6E-96
23 g2687.t7 Gene3D G3DSA:3.30.1330.20 - 198 247 3.6E-24
22 g2687.t7 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 248 301 3.8E-34
3 g2687.t7 PANTHER PTHR11588:SF292 TUBULIN ALPHA-1D CHAIN 2 198 6.4E-204
5 g2687.t7 PANTHER PTHR11588 TUBULIN 2 198 6.4E-204
4 g2687.t7 PANTHER PTHR11588:SF292 TUBULIN ALPHA-1D CHAIN 198 309 6.4E-204
6 g2687.t7 PANTHER PTHR11588 TUBULIN 198 309 6.4E-204
19 g2687.t7 PRINTS PR01161 Tubulin signature 10 30 5.1E-66
12 g2687.t7 PRINTS PR01162 Alpha-tubulin signature 18 33 9.3E-43
10 g2687.t7 PRINTS PR01162 Alpha-tubulin signature 45 58 9.3E-43
16 g2687.t7 PRINTS PR01161 Tubulin signature 53 72 5.1E-66
7 g2687.t7 PRINTS PR01162 Alpha-tubulin signature 88 101 9.3E-43
15 g2687.t7 PRINTS PR01161 Tubulin signature 95 106 5.1E-66
13 g2687.t7 PRINTS PR01161 Tubulin signature 108 132 5.1E-66
9 g2687.t7 PRINTS PR01162 Alpha-tubulin signature 120 128 9.3E-43
18 g2687.t7 PRINTS PR01161 Tubulin signature 134 152 5.1E-66
8 g2687.t7 PRINTS PR01162 Alpha-tubulin signature 148 160 9.3E-43
17 g2687.t7 PRINTS PR01161 Tubulin signature 153 174 5.1E-66
11 g2687.t7 PRINTS PR01162 Alpha-tubulin signature 161 172 9.3E-43
14 g2687.t7 PRINTS PR01161 Tubulin signature 178 191 5.1E-66
1 g2687.t7 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 198 6.2E-61
2 g2687.t7 Pfam PF03953 Tubulin C-terminal domain 196 256 2.1E-17
27 g2687.t7 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 142 148 -
28 g2687.t7 SMART SM00864 Tubulin_4 49 252 6.6E-45
20 g2687.t7 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 198 7.72E-82
21 g2687.t7 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 174 301 3.36E-46

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. There were no conditions that were differentially expressed