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.t17 TSS g2687.t17 19716871 19716871
chr_3 g2687 g2687.t17 isoform g2687.t17 19716989 19719666
chr_3 g2687 g2687.t17 exon g2687.t17.exon1 19716989 19716991
chr_3 g2687 g2687.t17 cds g2687.t17.CDS1 19716989 19716991
chr_3 g2687 g2687.t17 exon g2687.t17.exon2 19717306 19718837
chr_3 g2687 g2687.t17 cds g2687.t17.CDS2 19717306 19718655
chr_3 g2687 g2687.t17 exon g2687.t17.exon3 19719365 19719666
chr_3 g2687 g2687.t17 TTS g2687.t17 NA NA

Sequences

>g2687.t17 Gene=g2687 Length=1837
ATGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGT
TGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAATGCCATCTGACAAG
ACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAACTGGTGCAGGCAAA
CACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCGATGAAGTCCGCACT
GGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGCTGCC
AACAACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCGATTTGGTTTTGGAT
CGCATCCGTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCTTAATTTTCCACTCA
TTCGGTGGCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAACGTCTCTCAGTTGAT
TATGGCAAGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCACAAGTATCTACTGCT
GTTGTTGAACCATATAACTCAATCTTGACAACACATACAACTTTGGAACACTCTGACTGC
GCATTCATGGTCGATAACGAAGCTATCTATGACATCTGCCGTCGTAATTTGGACATTGAA
CGCCCAACATATACCAACTTGAATCGTTTGATTGGCCAGATTGTCTCATCGATCACCGCA
TCACTCCGTTTCGATGGTGCATTGAACGTCGATTTGACTGAATTCCAAACTAACTTGGTA
CCATATCCACGTATTCACTTCCCATTGGTTACATATGCCCCAGTCATCTCAGCTGAAAAA
GCTTACCATGAACAATTGAGCGTTGCTGAAATCACAAACGCTTGTTTCGAACCAGCCAAC
CAAATGGTCAAATGCGATCCACGTCATGGTAAATACATGGCTTGCTGCATGTTGTACAGA
GGTGATGTTGTACCAAAAGATGTCAATGCAGCCATTGCTACAATCAAGACAAAACGTACC
ATTCAATTTGTCGATTGGTGTCCAACTGGTTTCAAAGTTGGTATCAATTATCAACCACCA
ACTGTTGTTCCAGGCGGTGATTTGGCCAAGGTTCAACGCGCTGTTTGCATGTTGTCAAAC
ACAACTGCCATCGCTGAAGCATGGGCTCGTCTTGATCATAAATTCGATTTGATGTATGCC
AAGCGTGCATTCGTTCACTGGTATGTCGGTGAAGGTATGGAAGAAGGTGAATTCTCAGAA
GCTCGTGAGGATTTGGCCGCTTTGGAGAAAGATTATGAAGAAGTTGGCATGGACTCTGGC
GAGGGAGAAGGCGAAGGCGCAGAAGAATACTAAGAACAGTAATCTGACAAATTTCATGCT
TCGCATAATTGCTTCTCTCAAGATCGATAAAAATATAATAGTATGAACTTTGCTTGATAC
ACATTATTGTTTTAAAATATCTTAAACAAAATCCTGCAATTGAAAAAATAAAGCTACAGC
TTTAATATTTTGCTTTGCTTTTAACAAAAGGCATGAAATATGAAAGAAAACTCTAAATAG
AATGTGGGCATGATAGTTTGAAAAAATATGTTCATATTCAATTGGCACATAATGCAGAGG
AAATTAAGAAGAAGAATTTTTCTAAATTTAACTTTAAAAATGGTAGACATGAACATGTGC
CGAAACACAGGCAAGCATTGTTAGATCAATAAACCGTTAAAAAAACTTTATTTCTCCCTT
CCACTAAATTAAAATGCCGCTTATACGATCCTCTCTCTTTTTCAAAAATTTCCCCACCTC
ATACAAATAATAAAACAATCAAAATCGTTCAACGAGC

>g2687.t17 Gene=g2687 Length=450
MRECISVHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLD
RIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFAIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLVTYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCMLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDLAALEKDYEEVGMDSGEGEGEGAEEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
33 g2687.t17 CDD cd02186 alpha_tubulin 2 435 0.0
32 g2687.t17 Coils Coil Coil 418 438 -
31 g2687.t17 Gene3D G3DSA:3.40.50.1440 - 1 268 5.8E-133
30 g2687.t17 Gene3D G3DSA:3.30.1330.20 - 269 383 6.9E-68
29 g2687.t17 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 384 437 6.4E-34
3 g2687.t17 PANTHER PTHR11588:SF304 TUBULIN ALPHA CHAIN 2 445 0.0
4 g2687.t17 PANTHER PTHR11588 TUBULIN 2 445 0.0
22 g2687.t17 PRINTS PR01161 Tubulin signature 10 30 1.0E-90
16 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 18 33 6.5E-121
10 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 45 58 6.5E-121
21 g2687.t17 PRINTS PR01161 Tubulin signature 53 72 1.0E-90
15 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 88 101 6.5E-121
20 g2687.t17 PRINTS PR01161 Tubulin signature 95 106 1.0E-90
23 g2687.t17 PRINTS PR01161 Tubulin signature 108 132 1.0E-90
8 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 120 128 6.5E-121
25 g2687.t17 PRINTS PR01161 Tubulin signature 134 152 1.0E-90
7 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 148 160 6.5E-121
26 g2687.t17 PRINTS PR01161 Tubulin signature 153 174 1.0E-90
12 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 161 172 6.5E-121
19 g2687.t17 PRINTS PR01161 Tubulin signature 178 191 1.0E-90
24 g2687.t17 PRINTS PR01161 Tubulin signature 192 212 1.0E-90
6 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 214 226 6.5E-121
11 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 274 289 6.5E-121
5 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 321 342 6.5E-121
14 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 347 360 6.5E-121
17 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 360 379 6.5E-121
18 g2687.t17 PRINTS PR01161 Tubulin signature 380 408 1.0E-90
9 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 385 401 6.5E-121
13 g2687.t17 PRINTS PR01162 Alpha-tubulin signature 422 438 6.5E-121
1 g2687.t17 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 213 4.5E-68
2 g2687.t17 Pfam PF03953 Tubulin C-terminal domain 263 392 6.6E-53
34 g2687.t17 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 142 148 -
35 g2687.t17 SMART SM00864 Tubulin_4 49 246 1.2E-83
36 g2687.t17 SMART SM00865 Tubulin_C_4 248 393 1.2E-60
27 g2687.t17 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 244 1.83E-101
28 g2687.t17 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 246 437 1.92E-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

Pathway

  • This transcript belongs to the following pathways

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