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.t13 TSS g2687.t13 19716871 19716871
chr_3 g2687 g2687.t13 isoform g2687.t13 19716989 19718655
chr_3 g2687 g2687.t13 exon g2687.t13.exon1 19716989 19718362
chr_3 g2687 g2687.t13 cds g2687.t13.CDS1 19717408 19718362
chr_3 g2687 g2687.t13 exon g2687.t13.exon2 19718448 19718655
chr_3 g2687 g2687.t13 cds g2687.t13.CDS2 19718448 19718494
chr_3 g2687 g2687.t13 TTS g2687.t13 19718842 19718842

Sequences

>g2687.t13 Gene=g2687 Length=1582
ATGGTAAGTAACATAATTATCAAATAAAATTCTTGATAAATAAGTGTGAAAAATCTAAAA
ACATTTTGTTCAGTCCGTTAGGACGCCATTTTAGTTTTTTTCTGCTTAAAGTACTATAAA
TTTTAATGCATAAACTAATTTATCCTTTTCCTATCAAGTTAAATATTATATTGATAAACT
TTCTTACTAGATTTTTTTTCATTTATGCTATTTTCATACCACGCCCAATTTTCTTAACCA
AATCGATATTTTTTTATGATTTTTATGCTGATGACTCATCCAATTTTTTTCAATTTCTTT
CTCATTAAATACTATAGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAA
TCGGAAATGCCTGTTGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAA
TGCCATCTGACAAGACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAA
CTGGTGCAGGCAAACACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCG
ATGAAGTCCGCACTGGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTA
AGGAAGATGCTGCCAACAACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCG
ATTTGGTTTTGGATCGCATCCGTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCT
TAATTTTCCACTCATTCGGTGGCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAAC
GTCTCTCAGTTGATTATGGCAAGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCAC
AAGTATCTACTGCTGTTGTTGAACCATATAACTCAATCTTGACAACACATACAACTTTGG
AACACTCTGACTGCGCATTCATGGTCGATAACGAAGCTATCTATGACATCTGCCGTCGTA
ATTTGGACATTGAACGCCCAACATATACCAACTTGAATCGTTTGATTGGCCAGATTGTCT
CATCGATCACCGCATCACTCCGTTTCGATGGTGCATTGAACGTCGATTTGACTGAATTCC
AAACTAACTTGGTACCATATCCACGTATTCACTTCCCATTGGTTACATATGCCCCAGTCA
TCTCAGCTGAAAAAGCTTACCATGAACAATTGAGCGTTGCTGAAATCACAAACGCTTGTT
TCGAACCAGCCAACCAAATGGTCAAATGCGATCCACGTCATGGTAAATACATGGCTTGCT
GCATGTTGTACAGAGGTGATGTTGTACCAAAAGATGTCAATGCAGCCATTGCTACAATCA
AGACAAAACGTACCATTCAATTTGTCGATTGGTGTCCAACTGGTTTCAAAGTTGTGCCAT
CGCTGAAGCATGGGCTCGTCTTGATCATAAATTCGATTTGATGTATGCCAAGCGTGCATT
CGTTCACTGGTATGTCGGTGAAGGTATGGAAGAAGGTGAATTCTCAGAAGCTCGTGAGGA
TTTGGCCGCTTTGGAGAAAGATTATGAAGAAGTTGGCATGGACTCTGGCGAGGGAGAAGG
CGAAGGCGCAGAAGAATACTAA

>g2687.t13 Gene=g2687 Length=333
MPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITG
KEDAANNYARGHYTIGKEIVDLVLDRIRKLADQCTGLQGFLIFHSFGGGTGSGFTSLLME
RLSVDYGKKSKLEFAIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRR
NLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLVTYAPV
ISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCMLYRGDVVPKDVNAAIATI
KTKRTIQFVDWCPTGFKVVPSLKHGLVLIINSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g2687.t13 CDD cd02186 alpha_tubulin 1 318 0.0
24 g2687.t13 Gene3D G3DSA:3.40.50.1440 - 1 233 1.5E-110
23 g2687.t13 Gene3D G3DSA:3.30.1330.20 - 234 326 1.5E-48
3 g2687.t13 PANTHER PTHR11588:SF304 TUBULIN ALPHA CHAIN 4 319 8.1E-225
4 g2687.t13 PANTHER PTHR11588 TUBULIN 4 319 8.1E-225
7 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 10 23 1.3E-69
18 g2687.t13 PRINTS PR01161 Tubulin signature 18 37 1.5E-65
12 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 53 66 1.3E-69
16 g2687.t13 PRINTS PR01161 Tubulin signature 60 71 1.5E-65
17 g2687.t13 PRINTS PR01161 Tubulin signature 73 97 1.5E-65
5 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 85 93 1.3E-69
20 g2687.t13 PRINTS PR01161 Tubulin signature 99 117 1.5E-65
10 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 113 125 1.3E-69
15 g2687.t13 PRINTS PR01161 Tubulin signature 118 139 1.5E-65
13 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 126 137 1.3E-69
19 g2687.t13 PRINTS PR01161 Tubulin signature 143 156 1.5E-65
14 g2687.t13 PRINTS PR01161 Tubulin signature 157 177 1.5E-65
9 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 179 191 1.3E-69
11 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 239 254 1.3E-69
8 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 286 307 1.3E-69
6 g2687.t13 PRINTS PR01162 Alpha-tubulin signature 312 325 1.3E-69
1 g2687.t13 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 12 178 4.7E-54
2 g2687.t13 Pfam PF03953 Tubulin C-terminal domain 228 319 4.0E-39
26 g2687.t13 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 107 113 -
27 g2687.t13 SMART SM00864 Tubulin_4 14 211 1.2E-83
28 g2687.t13 SMART SM00865 Tubulin_C_4 213 331 8.1E-34
21 g2687.t13 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 4 209 3.01E-83
22 g2687.t13 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 211 331 3.36E-47

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