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.t10 TSS g2687.t10 19716871 19716871
chr_3 g2687 g2687.t10 isoform g2687.t10 19716989 19718655
chr_3 g2687 g2687.t10 exon g2687.t10.exon1 19716989 19716991
chr_3 g2687 g2687.t10 cds g2687.t10.CDS1 19716989 19716991
chr_3 g2687 g2687.t10 exon g2687.t10.exon2 19717306 19718079
chr_3 g2687 g2687.t10 cds g2687.t10.CDS2 19717306 19718079
chr_3 g2687 g2687.t10 exon g2687.t10.exon3 19718262 19718655
chr_3 g2687 g2687.t10 cds g2687.t10.CDS3 19718262 19718267
chr_3 g2687 g2687.t10 TTS g2687.t10 19718842 19718842

Sequences

>g2687.t10 Gene=g2687 Length=1171
ATGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGT
TGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAATGCCATCTGACAAG
ACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAACTGGTGCAGGCAAA
CACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCGATGAAGTCCGCACT
GGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGCTGCC
AACAACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCGATTTGGTTTTGGAT
CGCATCCGTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCTTAATTTTCCACTCA
TTCGGTGGCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAACGTCTCTCAGTTGAT
TATGGCAAGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCACAAGTATCTACTGCT
GTTGTTGAACCATATAACTCAATCTTGACAACACATACAACTTTGGAACACTCTGACTGC
GCATTCATGGTCGATAACGAAGCTATCTATGACATCTGCCGTCGTAATTTGGACATTGAA
CGCCCAACATATACCAACTTGAATCGTTTGATTGGCCAGATTGTCTCATCGATCACCGCA
TCACTCCGTTTCGATGGTGCATTGAACGTCGATTTGACTGAATTCCAAACTAACTTGAGG
TGATGTTGTACCAAAAGATGTCAATGCAGCCATTGCTACAATCAAGACAAAACGTACCAT
TCAATTTGTCGATTGGTGTCCAACTGGTTTCAAAGTTGGTATCAATTATCAACCACCAAC
TGTTGTTCCAGGCGGTGATTTGGCCAAGGTTCAACGCGCTGTTTGCATGTTGTCAAACAC
AACTGCCATCGCTGAAGCATGGGCTCGTCTTGATCATAAATTCGATTTGATGTATGCCAA
GCGTGCATTCGTTCACTGGTATGTCGGTGAAGGTATGGAAGAAGGTGAATTCTCAGAAGC
TCGTGAGGATTTGGCCGCTTTGGAGAAAGATTATGAAGAAGTTGGCATGGACTCTGGCGA
GGGAGAAGGCGAAGGCGCAGAAGAATACTAA

>g2687.t10 Gene=g2687 Length=260
MRECISVHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLD
RIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFAIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g2687.t10 Gene3D G3DSA:3.40.50.1440 - 1 260 6.8E-127
2 g2687.t10 PANTHER PTHR11588:SF292 TUBULIN ALPHA-1D CHAIN 2 259 2.4E-176
3 g2687.t10 PANTHER PTHR11588 TUBULIN 2 259 2.4E-176
14 g2687.t10 PRINTS PR01161 Tubulin signature 10 30 2.8E-77
10 g2687.t10 PRINTS PR01162 Alpha-tubulin signature 18 33 1.3E-51
8 g2687.t10 PRINTS PR01162 Alpha-tubulin signature 45 58 1.3E-51
13 g2687.t10 PRINTS PR01161 Tubulin signature 53 72 2.8E-77
4 g2687.t10 PRINTS PR01162 Alpha-tubulin signature 88 101 1.3E-51
12 g2687.t10 PRINTS PR01161 Tubulin signature 95 106 2.8E-77
15 g2687.t10 PRINTS PR01161 Tubulin signature 108 132 2.8E-77
7 g2687.t10 PRINTS PR01162 Alpha-tubulin signature 120 128 1.3E-51
17 g2687.t10 PRINTS PR01161 Tubulin signature 134 152 2.8E-77
6 g2687.t10 PRINTS PR01162 Alpha-tubulin signature 148 160 1.3E-51
18 g2687.t10 PRINTS PR01161 Tubulin signature 153 174 2.8E-77
9 g2687.t10 PRINTS PR01162 Alpha-tubulin signature 161 172 1.3E-51
11 g2687.t10 PRINTS PR01161 Tubulin signature 178 191 2.8E-77
16 g2687.t10 PRINTS PR01161 Tubulin signature 192 212 2.8E-77
5 g2687.t10 PRINTS PR01162 Alpha-tubulin signature 214 226 1.3E-51
1 g2687.t10 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 213 9.0E-69
21 g2687.t10 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 142 148 -
20 g2687.t10 SMART SM00864 Tubulin_4 49 246 1.2E-83
19 g2687.t10 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 245 3.14E-102

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