Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin alpha-2 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_4 g14768 g14768.t1 TTS g14768.t1 2249284 2249284
chr_4 g14768 g14768.t1 isoform g14768.t1 2249548 2251448
chr_4 g14768 g14768.t1 exon g14768.t1.exon1 2249548 2249994
chr_4 g14768 g14768.t1 cds g14768.t1.CDS1 2249548 2249994
chr_4 g14768 g14768.t1 exon g14768.t1.exon2 2250144 2251043
chr_4 g14768 g14768.t1 cds g14768.t1.CDS2 2250144 2251043
chr_4 g14768 g14768.t1 exon g14768.t1.exon3 2251437 2251448
chr_4 g14768 g14768.t1 cds g14768.t1.CDS3 2251437 2251448
chr_4 g14768 g14768.t1 TSS g14768.t1 NA NA

Sequences

>g14768.t1 Gene=g14768 Length=1359
ATGAAATGTATGCGTGAATGTATTTCAGTCCATATCGGTCAAGCTGGTGTTCAAATTGGC
AATGCCTGTTGGGAACTTTACTGTCTTGAACATGGAATTCAGCCAGATGGTCAAATGCCA
TCAGACAAGACAATTGGAGGTGGTGATGATTCATTTAATACTTTCTTCTCTGAAACTGGA
AGTGGCAAGCATGTTCCACGTGCTGTCTTTGTTGACTTGGAACCAACTGTAGTTGATGAA
GTTCGTACTGGAACTTATCGTCAACTTTTTCATCCTGAACAATTGATTACTGGCAAAGAA
GATGCTGCCAATAATTATGCTCGTGGTCATTATACAATTGGCAAAGAAATTGTCGACATT
GTTTTGGATCGCATTCGTAAATTGGCTGATCAATGTACTGGCTTGCAAGGATTTCTTGTT
TTCCATTCATTCGGTGGTGGCACTGGATCAGGTTTCACATCACTTTTAATGGAACGTTTG
TCAGTTGATTATGGCAAGAAGTCAAAACTTGAATTCTCAATCTATCCAGCACCACAAGTT
TCAACTGCTGTTGTTGAGCCTTACAATTCAATTCTCACAACTCATACAACTTTGGAACAT
TCCGATTGTGCATTCATGGTCGATAATGAAGCCATTTATGACATTTGTCGCCGAAATCTT
GACATTGAACGTCCAACTTATACAAATTTGAACCGCTTGATTGGTCAAATTGTTTCATCA
ATAACTGCATCACTCAGATTCGACGGTGCATTAAATGTCGACTTGACAGAATTCCAAACC
AACTTGGTGCCTTATCCACGTATTCATTTCCCATTGGCAACTTATGCACCAGTTATTTCA
GCTGAAAAAGCTTATCATGAACAATTGACTGTTGCTGAAATTACAAATGCTTGCTTTGAG
CCAGCTAATCAGATGGTAAAATGCGATCCACGCCACGGCAAATACATGGCCTGCTGCATG
TTGTACAGAGGTGATGTTGTTCCAAAAGATGTCAATGCAGCTATTGCTACAATCAAGACC
AAGCGAAGCATTCAATTTGTTGATTGGTGTCCAACTGGTTTCAAAGTCGGCATCAACTAT
CAGCCACCAACTGTCGTTCCTGGTGGTGATTTGGCTAAAGTTCAACGTGCTGTTTGCATG
TTGTCAAATACAACAGCTATTGCTGAAGCTTGGGCTCGTTTGGATCATAAATTTGATTTA
ATGTATGCCAAGCGTGCTTTTGTCCATTGGTATGTTGGTGAAGGTATGGAAGAAGGCGAA
TTCTCTGAAGCACGTGAAGATTTGGCTGCTTTGGAGAAAGATTATGAGGAAGTTGGTGTT
GATTCAACTGAAGAAGTCGGTGAAGGAGACGAATACTAA

>g14768.t1 Gene=g14768 Length=452
MKCMRECISVHIGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETG
SGKHVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDI
VLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQV
STAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSS
ITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLTVAEITNACFE
PANQMVKCDPRHGKYMACCMLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINY
QPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGE
FSEAREDLAALEKDYEEVGVDSTEEVGEGDEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g14768.t1 CDD cd02186 alpha_tubulin 5 438 0.0
31 g14768.t1 Gene3D G3DSA:3.40.50.1440 - 4 271 8.4E-133
30 g14768.t1 Gene3D G3DSA:3.30.1330.20 - 272 386 7.4E-68
29 g14768.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 387 440 3.4E-34
3 g14768.t1 PANTHER PTHR11588:SF64 TUBULIN ALPHA-1C CHAIN 5 451 0.0
4 g14768.t1 PANTHER PTHR11588 TUBULIN 5 451 0.0
25 g14768.t1 PRINTS PR01161 Tubulin signature 13 33 5.4E-91
6 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 21 36 3.8E-120
11 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 48 61 3.8E-120
20 g14768.t1 PRINTS PR01161 Tubulin signature 56 75 5.4E-91
10 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 91 104 3.8E-120
19 g14768.t1 PRINTS PR01161 Tubulin signature 98 109 5.4E-91
23 g14768.t1 PRINTS PR01161 Tubulin signature 111 135 5.4E-91
13 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 123 131 3.8E-120
21 g14768.t1 PRINTS PR01161 Tubulin signature 137 155 5.4E-91
12 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 151 163 3.8E-120
26 g14768.t1 PRINTS PR01161 Tubulin signature 156 177 5.4E-91
7 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 164 175 3.8E-120
24 g14768.t1 PRINTS PR01161 Tubulin signature 181 194 5.4E-91
22 g14768.t1 PRINTS PR01161 Tubulin signature 195 215 5.4E-91
15 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 217 229 3.8E-120
16 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 277 292 3.8E-120
14 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 324 345 3.8E-120
9 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 350 363 3.8E-120
17 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 363 382 3.8E-120
18 g14768.t1 PRINTS PR01161 Tubulin signature 383 411 5.4E-91
5 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 388 404 3.8E-120
8 g14768.t1 PRINTS PR01162 Alpha-tubulin signature 425 441 3.8E-120
1 g14768.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 6 216 2.0E-68
2 g14768.t1 Pfam PF03953 Tubulin C-terminal domain 266 395 1.7E-52
33 g14768.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 145 151 -
34 g14768.t1 SMART SM00864 Tubulin_4 52 249 2.3E-83
35 g14768.t1 SMART SM00865 Tubulin_C_4 251 396 3.6E-61
27 g14768.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 4 247 2.09E-101
28 g14768.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 249 439 3.66E-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