Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin alpha-1A 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.t3 TTS g14768.t3 2249284 2249284
chr_4 g14768 g14768.t3 isoform g14768.t3 2250152 2251043
chr_4 g14768 g14768.t3 exon g14768.t3.exon1 2250152 2251043
chr_4 g14768 g14768.t3 cds g14768.t3.CDS1 2250153 2250941
chr_4 g14768 g14768.t3 TSS g14768.t3 NA NA

Sequences

>g14768.t3 Gene=g14768 Length=892
CGTGAATGTATTTCAGTCCATATCGGTCAAGCTGGTGTTCAAATTGGCAATGCCTGTTGG
GAACTTTACTGTCTTGAACATGGAATTCAGCCAGATGGTCAAATGCCATCAGACAAGACA
ATTGGAGGTGGTGATGATTCATTTAATACTTTCTTCTCTGAAACTGGAAGTGGCAAGCAT
GTTCCACGTGCTGTCTTTGTTGACTTGGAACCAACTGTAGTTGATGAAGTTCGTACTGGA
ACTTATCGTCAACTTTTTCATCCTGAACAATTGATTACTGGCAAAGAAGATGCTGCCAAT
AATTATGCTCGTGGTCATTATACAATTGGCAAAGAAATTGTCGACATTGTTTTGGATCGC
ATTCGTAAATTGGCTGATCAATGTACTGGCTTGCAAGGATTTCTTGTTTTCCATTCATTC
GGTGGTGGCACTGGATCAGGTTTCACATCACTTTTAATGGAACGTTTGTCAGTTGATTAT
GGCAAGAAGTCAAAACTTGAATTCTCAATCTATCCAGCACCACAAGTTTCAACTGCTGTT
GTTGAGCCTTACAATTCAATTCTCACAACTCATACAACTTTGGAACATTCCGATTGTGCA
TTCATGGTCGATAATGAAGCCATTTATGACATTTGTCGCCGAAATCTTGACATTGAACGT
CCAACTTATACAAATTTGAACCGCTTGATTGGTCAAATTGTTTCATCAATAACTGCATCA
CTCAGATTCGACGGTGCATTAAATGTCGACTTGACAGAATTCCAAACCAACTTGGTGCCT
TATCCACGTATTCATTTCCCATTGGCAACTTATGCACCAGTTATTTCAGCTGAAAAAGCT
TATCATGAACAATTGACTGTTGCTGAAATTACAAATGCTTGCTTTGAGCCAG

>g14768.t3 Gene=g14768 Length=263
MPSDKTIGGGDDSFNTFFSETGSGKHVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITG
KEDAANNYARGHYTIGKEIVDIVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLME
RLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRR
NLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPV
ISAEKAYHEQLTVAEITNACFEP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g14768.t3 Gene3D G3DSA:3.40.50.1440 - 1 230 7.8E-111
23 g14768.t3 Gene3D G3DSA:3.30.1330.20 - 231 263 1.1E-9
3 g14768.t3 PANTHER PTHR11588:SF64 TUBULIN ALPHA-1C CHAIN 4 263 1.6E-180
4 g14768.t3 PANTHER PTHR11588 TUBULIN 4 263 1.6E-180
9 g14768.t3 PRINTS PR01162 Alpha-tubulin signature 10 23 9.7E-51
16 g14768.t3 PRINTS PR01161 Tubulin signature 18 37 1.9E-66
11 g14768.t3 PRINTS PR01162 Alpha-tubulin signature 53 66 9.7E-51
14 g14768.t3 PRINTS PR01161 Tubulin signature 60 71 1.9E-66
15 g14768.t3 PRINTS PR01161 Tubulin signature 73 97 1.9E-66
8 g14768.t3 PRINTS PR01162 Alpha-tubulin signature 85 93 9.7E-51
18 g14768.t3 PRINTS PR01161 Tubulin signature 99 117 1.9E-66
7 g14768.t3 PRINTS PR01162 Alpha-tubulin signature 113 125 9.7E-51
13 g14768.t3 PRINTS PR01161 Tubulin signature 118 139 1.9E-66
10 g14768.t3 PRINTS PR01162 Alpha-tubulin signature 126 137 9.7E-51
17 g14768.t3 PRINTS PR01161 Tubulin signature 143 156 1.9E-66
12 g14768.t3 PRINTS PR01161 Tubulin signature 157 177 1.9E-66
5 g14768.t3 PRINTS PR01162 Alpha-tubulin signature 179 191 9.7E-51
6 g14768.t3 PRINTS PR01162 Alpha-tubulin signature 239 254 9.7E-51
1 g14768.t3 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 12 178 5.8E-55
2 g14768.t3 Pfam PF03953 Tubulin C-terminal domain 228 263 1.0E-8
22 g14768.t3 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 107 113 -
21 g14768.t3 SMART SM00864 Tubulin_4 14 211 2.3E-83
19 g14768.t3 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 4 210 1.01E-83
20 g14768.t3 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 214 263 1.31E-16

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