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.t4 TSS g2687.t4 19716871 19716871
chr_3 g2687 g2687.t4 isoform g2687.t4 19716989 19718174
chr_3 g2687 g2687.t4 exon g2687.t4.exon1 19716989 19716995
chr_3 g2687 g2687.t4 exon g2687.t4.exon2 19717306 19718174
chr_3 g2687 g2687.t4 cds g2687.t4.CDS1 19717408 19718172
chr_3 g2687 g2687.t4 TTS g2687.t4 19718842 19718842

Sequences

>g2687.t4 Gene=g2687 Length=876
ATGGTAACGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGC
CTGTTGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAATGCCATCTGA
CAAGACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAACTGGTGCAGG
CAAACACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCGATGAAGTCCG
CACTGGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGC
TGCCAACAACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCGATTTGGTTTT
GGATCGCATCCGTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCTTAATTTTCCA
CTCATTCGGTGGCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAACGTCTCTCAGT
TGATTATGGCAAGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCACAAGTATCTAC
TGCTGTTGTTGAACCATATAACTCAATCTTGACAACACATACAACTTTGGAACACTCTGA
CTGCGCATTCATGGTCGATAACGAAGCTATCTATGACATCTGCCGTCGTAATTTGGACAT
TGAACGCCCAACATATACCAACTTGAATCGTTTGATTGGCCAGATTGTCTCATCGATCAC
CGCATCACTCCGTTTCGATGGTGCATTGAACGTCGATTTGACTGAATTCCAAACTAACTT
GGTACCATATCCACGTATTCACTTCCCATTGGTTACATATGCCCCAGTCATCTCAGCTGA
AAAAGCTTACCATGAACAATTGAGCGTTGCTGAAAT

>g2687.t4 Gene=g2687 Length=255
MPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITG
KEDAANNYARGHYTIGKEIVDLVLDRIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLME
RLSVDYGKKSKLEFAIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRR
NLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLVTYAPV
ISAEKAYHEQLSVAE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g2687.t4 Gene3D G3DSA:3.40.50.1440 - 1 229 6.0E-111
22 g2687.t4 Gene3D G3DSA:3.30.1330.20 - 230 255 1.4E-5
2 g2687.t4 PANTHER PTHR11588:SF349 TUBULIN ALPHA CHAIN 4 255 1.3E-173
3 g2687.t4 PANTHER PTHR11588 TUBULIN 4 255 1.3E-173
8 g2687.t4 PRINTS PR01162 Alpha-tubulin signature 10 23 2.6E-51
15 g2687.t4 PRINTS PR01161 Tubulin signature 18 37 3.4E-66
10 g2687.t4 PRINTS PR01162 Alpha-tubulin signature 53 66 2.6E-51
13 g2687.t4 PRINTS PR01161 Tubulin signature 60 71 3.4E-66
14 g2687.t4 PRINTS PR01161 Tubulin signature 73 97 3.4E-66
7 g2687.t4 PRINTS PR01162 Alpha-tubulin signature 85 93 2.6E-51
17 g2687.t4 PRINTS PR01161 Tubulin signature 99 117 3.4E-66
6 g2687.t4 PRINTS PR01162 Alpha-tubulin signature 113 125 2.6E-51
12 g2687.t4 PRINTS PR01161 Tubulin signature 118 139 3.4E-66
9 g2687.t4 PRINTS PR01162 Alpha-tubulin signature 126 137 2.6E-51
16 g2687.t4 PRINTS PR01161 Tubulin signature 143 156 3.4E-66
11 g2687.t4 PRINTS PR01161 Tubulin signature 157 177 3.4E-66
4 g2687.t4 PRINTS PR01162 Alpha-tubulin signature 179 191 2.6E-51
5 g2687.t4 PRINTS PR01162 Alpha-tubulin signature 239 254 2.6E-51
1 g2687.t4 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 12 178 2.2E-54
21 g2687.t4 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 107 113 -
20 g2687.t4 SMART SM00864 Tubulin_4 14 211 1.2E-83
18 g2687.t4 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 4 210 1.31E-83
19 g2687.t4 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 211 255 2.17E-13

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