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.t18 TSS g2687.t18 19716871 19716871
chr_3 g2687 g2687.t18 isoform g2687.t18 19717306 19718837
chr_3 g2687 g2687.t18 exon g2687.t18.exon1 19717306 19718837
chr_3 g2687 g2687.t18 cds g2687.t18.CDS1 19717408 19718655
chr_3 g2687 g2687.t18 TTS g2687.t18 19718842 19718842

Sequences

>g2687.t18 Gene=g2687 Length=1532
CGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGTTGG
GAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAATGCCATCTGACAAGACA
ATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAACTGGTGCAGGCAAACAC
GTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCGATGAAGTCCGCACTGGA
ACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGCTGCCAAC
AACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCGATTTGGTTTTGGATCGC
ATCCGTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCTTAATTTTCCACTCATTC
GGTGGCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAACGTCTCTCAGTTGATTAT
GGCAAGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCACAAGTATCTACTGCTGTT
GTTGAACCATATAACTCAATCTTGACAACACATACAACTTTGGAACACTCTGACTGCGCA
TTCATGGTCGATAACGAAGCTATCTATGACATCTGCCGTCGTAATTTGGACATTGAACGC
CCAACATATACCAACTTGAATCGTTTGATTGGCCAGATTGTCTCATCGATCACCGCATCA
CTCCGTTTCGATGGTGCATTGAACGTCGATTTGACTGAATTCCAAACTAACTTGGTACCA
TATCCACGTATTCACTTCCCATTGGTTACATATGCCCCAGTCATCTCAGCTGAAAAAGCT
TACCATGAACAATTGAGCGTTGCTGAAATCACAAACGCTTGTTTCGAACCAGCCAACCAA
ATGGTCAAATGCGATCCACGTCATGGTAAATACATGGCTTGCTGCATGTTGTACAGAGGT
GATGTTGTACCAAAAGATGTCAATGCAGCCATTGCTACAATCAAGACAAAACGTACCATT
CAATTTGTCGATTGGTGTCCAACTGGTTTCAAAGTTGGTATCAATTATCAACCACCAACT
GTTGTTCCAGGCGGTGATTTGGCCAAGGTTCAACGCGCTGTTTGCATGTTGTCAAACACA
ACTGCCATCGCTGAAGCATGGGCTCGTCTTGATCATAAATTCGATTTGATGTATGCCAAG
CGTGCATTCGTTCACTGGTATGTCGGTGAAGGTATGGAAGAAGGTGAATTCTCAGAAGCT
CGTGAGGATTTGGCCGCTTTGGAGAAAGATTATGAAGAAGTTGGCATGGACTCTGGCGAG
GGAGAAGGCGAAGGCGCAGAAGAATACTAAGAACAGTAATCTGACAAATTTCATGCTTCG
CATAATTGCTTCTCTCAAGATCGATAAAAATATAATAGTATGAACTTTGCTTGATACACA
TTATTGTTTTAAAATATCTTAAACAAAATCCTGCAATTGAAAAAATAAAGCTACAGCTTT
AATATTTTGCTTTGCTTTTAACAAAAGGCATG

>g2687.t18 Gene=g2687 Length=415
MPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITG
KEDAANNYARGHYTIGKEIVDLVLDRIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLME
RLSVDYGKKSKLEFAIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRR
NLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLVTYAPV
ISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCMLYRGDVVPKDVNAAIATI
KTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKF
DLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGMDSGEGEGEGAEEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
31 g2687.t18 CDD cd02186 alpha_tubulin 1 400 0.0
30 g2687.t18 Coils Coil Coil 383 403 -
29 g2687.t18 Gene3D G3DSA:3.40.50.1440 - 1 233 2.8E-110
28 g2687.t18 Gene3D G3DSA:3.30.1330.20 - 234 348 5.9E-68
27 g2687.t18 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 349 402 5.7E-34
3 g2687.t18 PANTHER PTHR11588:SF304 TUBULIN ALPHA CHAIN 4 410 1.0E-291
4 g2687.t18 PANTHER PTHR11588 TUBULIN 4 410 1.0E-291
7 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 10 23 3.7E-111
23 g2687.t18 PRINTS PR01161 Tubulin signature 18 37 5.2E-80
15 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 53 66 3.7E-111
20 g2687.t18 PRINTS PR01161 Tubulin signature 60 71 5.2E-80
21 g2687.t18 PRINTS PR01161 Tubulin signature 73 97 5.2E-80
5 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 85 93 3.7E-111
22 g2687.t18 PRINTS PR01161 Tubulin signature 99 117 5.2E-80
11 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 113 125 3.7E-111
19 g2687.t18 PRINTS PR01161 Tubulin signature 118 139 5.2E-80
16 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 126 137 3.7E-111
24 g2687.t18 PRINTS PR01161 Tubulin signature 143 156 5.2E-80
18 g2687.t18 PRINTS PR01161 Tubulin signature 157 177 5.2E-80
10 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 179 191 3.7E-111
12 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 239 254 3.7E-111
9 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 286 307 3.7E-111
6 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 312 325 3.7E-111
14 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 325 344 3.7E-111
17 g2687.t18 PRINTS PR01161 Tubulin signature 345 373 5.2E-80
8 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 350 366 3.7E-111
13 g2687.t18 PRINTS PR01162 Alpha-tubulin signature 387 403 3.7E-111
1 g2687.t18 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 12 178 8.0E-54
2 g2687.t18 Pfam PF03953 Tubulin C-terminal domain 228 357 5.7E-53
32 g2687.t18 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 107 113 -
33 g2687.t18 SMART SM00864 Tubulin_4 14 211 1.2E-83
34 g2687.t18 SMART SM00865 Tubulin_C_4 213 358 1.2E-60
25 g2687.t18 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 4 209 5.63E-83
26 g2687.t18 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 211 402 1.59E-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