Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin alpha 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_1 g10473 g10473.t1 TSS g10473.t1 10060676 10060676
chr_1 g10473 g10473.t1 isoform g10473.t1 10060775 10062235
chr_1 g10473 g10473.t1 exon g10473.t1.exon1 10060775 10060999
chr_1 g10473 g10473.t1 cds g10473.t1.CDS1 10060775 10060999
chr_1 g10473 g10473.t1 exon g10473.t1.exon2 10061050 10061477
chr_1 g10473 g10473.t1 cds g10473.t1.CDS2 10061050 10061477
chr_1 g10473 g10473.t1 exon g10473.t1.exon3 10061536 10062235
chr_1 g10473 g10473.t1 cds g10473.t1.CDS3 10061536 10062235
chr_1 g10473 g10473.t1 TTS g10473.t1 NA NA

Sequences

>g10473.t1 Gene=g10473 Length=1353
ATGGTATTTTCAAACAGAGAAACAATTTCAATTCACCTTGGTCAAGCTGGATGTCAACTA
GCTAGTGCAACATGGGAGCTTTATTGCCTTGAACATGGAATTAAATTTGATGGGTCAATG
AATGACTGTGCAGTCAATGAAGAAAATTGTTTTAAAACATTTTTTTGTGAATCACAAACT
GGGAAATATGTACCAAGAGCCATTTTAGTGGACACTGAACCAACTGTTGTTGATGAAATT
CGTAATGGAACTTTTAAGTGTCTTTTTCATCCTGACATGATGATCAATAGTAAAGAAGAT
GCAGCAAATAATTTCGCGCGTGGTTTTAATGCAATTGGTCAGGAAATTTTACCAGCAGTT
TTAAATTCAGTTCGTAAATCAGCTGAACAATCAAACAGCTTGCAAGGATTTTTTGTATTT
CATAGCTTTGGTGGAGGTACAGGCAGCGGCTTTTCTGCACTTTTAATGGAAGCTTTAAAT
GACGAATTTGGAAAGAAAAGCAAACTGCAAATTTCAATTTATCCATCGCCCCAAATATGT
ACAGCGATTGTTGAGCCTTATAATTCAGTTCTTACCACTCATTACTCAATGGACAATGTC
GATTGTGCATTCATTTTTGACAACCAAGCTATCTATGACATTTGCAAGAACAAGCTTAAC
ATCGAAAGTCCAAGTTATATACATCTGAATAGACTTATTTCACAAGTAGTTTCAAGCATC
ACGGCATCACTACGATTTAGCGGAGCTCTCAATGTCGACATGAATGAGTTTCAAACTAAT
TTAGTGCCATATCCTCGCATTCATTTTCCATTAGCAAGCTATGCTCCTTTTATCCCTATT
TCTAGAGCTGTTCATGAACAAGTGACTGTCAATGATTTAACATCAAATCTTTTTAAGAAT
GAAAATCAAATGGTAAAATGTGATACAAGTCAAGGAAAGTATATGGCTTGTTGTATTCTT
TATCGTGGTGACGTTGTCCCAAAAGATGTCAATTCAGCCATTTCAGAAGTAAAATCAAAA
CGAGCTTTGCAATTTGTTGATTGGTCACCAGCTGGATTTAAAATTGGTATTAATTGCAAG
TCACCAACAATCGTTGATGGAGGAGATTTGGCACGTGTAAATAAAAGTTGTAGTATGTTA
GCCTCAACGACAGCAATTGCTCAAGCTTGGGCGACAATAGATAGAAAATTCGACATGATG
TTTGCAAAACGTGCATTTTTACATTGGTACGTTGGTGAAGGATTAGATGAATTGAGCTTT
TGTGAAGCAAGAGAAAACCTAGCAGCTTTGGAAATGGACTATAAAGAAGCAGGCACAGAC
ACTTGTGATTTAGAAGGAATTAATTTTAAATAA

>g10473.t1 Gene=g10473 Length=450
MVFSNRETISIHLGQAGCQLASATWELYCLEHGIKFDGSMNDCAVNEENCFKTFFCESQT
GKYVPRAILVDTEPTVVDEIRNGTFKCLFHPDMMINSKEDAANNFARGFNAIGQEILPAV
LNSVRKSAEQSNSLQGFFVFHSFGGGTGSGFSALLMEALNDEFGKKSKLQISIYPSPQIC
TAIVEPYNSVLTTHYSMDNVDCAFIFDNQAIYDICKNKLNIESPSYIHLNRLISQVVSSI
TASLRFSGALNVDMNEFQTNLVPYPRIHFPLASYAPFIPISRAVHEQVTVNDLTSNLFKN
ENQMVKCDTSQGKYMACCILYRGDVVPKDVNSAISEVKSKRALQFVDWSPAGFKIGINCK
SPTIVDGGDLARVNKSCSMLASTTAIAQAWATIDRKFDMMFAKRAFLHWYVGEGLDELSF
CEARENLAALEMDYKEAGTDTCDLEGINFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g10473.t1 CDD cd02186 alpha_tubulin 6 436 0.0
31 g10473.t1 Gene3D G3DSA:3.40.50.1440 - 5 270 2.9E-110
30 g10473.t1 Gene3D G3DSA:3.30.1330.20 - 271 385 4.9E-48
29 g10473.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 386 448 1.1E-25
3 g10473.t1 PANTHER PTHR11588:SF248 AT04270P 6 442 1.3E-215
4 g10473.t1 PANTHER PTHR11588 TUBULIN 6 442 1.3E-215
23 g10473.t1 PRINTS PR01161 Tubulin signature 14 34 4.1E-70
7 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 22 37 9.4E-67
10 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 47 60 9.4E-67
26 g10473.t1 PRINTS PR01161 Tubulin signature 55 74 4.1E-70
6 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 90 103 9.4E-67
21 g10473.t1 PRINTS PR01161 Tubulin signature 97 108 4.1E-70
18 g10473.t1 PRINTS PR01161 Tubulin signature 110 134 4.1E-70
13 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 122 130 9.4E-67
25 g10473.t1 PRINTS PR01161 Tubulin signature 136 154 4.1E-70
9 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 150 162 9.4E-67
19 g10473.t1 PRINTS PR01161 Tubulin signature 155 176 4.1E-70
15 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 163 174 9.4E-67
20 g10473.t1 PRINTS PR01161 Tubulin signature 180 193 4.1E-70
22 g10473.t1 PRINTS PR01161 Tubulin signature 194 214 4.1E-70
5 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 216 228 9.4E-67
17 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 276 291 9.4E-67
8 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 323 344 9.4E-67
14 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 349 362 9.4E-67
12 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 362 381 9.4E-67
24 g10473.t1 PRINTS PR01161 Tubulin signature 382 410 4.1E-70
11 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 387 403 9.4E-67
16 g10473.t1 PRINTS PR01162 Alpha-tubulin signature 424 440 9.4E-67
1 g10473.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 7 216 2.3E-60
2 g10473.t1 Pfam PF03953 Tubulin C-terminal domain 265 394 6.6E-43
33 g10473.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 144 150 -
34 g10473.t1 SMART SM00864 Tubulin_4 51 248 2.6E-64
35 g10473.t1 SMART SM00865 Tubulin_C_4 250 395 1.8E-35
27 g10473.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 6 246 1.96E-83
28 g10473.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 248 440 2.35E-72

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