Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin beta-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_2 g8705 g8705.t1 isoform g8705.t1 32374633 32376052
chr_2 g8705 g8705.t1 exon g8705.t1.exon1 32374633 32375940
chr_2 g8705 g8705.t1 cds g8705.t1.CDS1 32374633 32375940
chr_2 g8705 g8705.t1 exon g8705.t1.exon2 32375996 32376052
chr_2 g8705 g8705.t1 cds g8705.t1.CDS2 32375996 32376052
chr_2 g8705 g8705.t1 TSS g8705.t1 NA NA
chr_2 g8705 g8705.t1 TTS g8705.t1 NA NA

Sequences

>g8705.t1 Gene=g8705 Length=1365
ATGCGAGAAATTGTTTCAATTCAAATTGGTCAATGTGGCAATAAAATTGGTGAAAAGTTT
TGGGAAATTATTTCGGAAGAACATAACATTAACAGATGTGGACATTTTTATGGAAATTCT
TATCTCCCATATCAACGTTTGGGTGTTTATTATGAAACAGGACCGCAAGAAATTTTTGTG
CCACGATCTATTTTAGTTGACCTCGATCAAGCGTCACTTAATTCAGTCAAGTGCGGTCTT
TATGGTCGAATTTTCAATCCTGATTGTTTTGTTGTTGGTCGATGTGGTGCTGGTAATAAT
TGGGCAAGAGGTCATTACACAGAAGGTGCAGAATTAATTGAGAGTGTTTTGGATGTGACA
AGAAAGCAAGTCGAATGTTGTGATTGCTTTCAAGGTTTTCAAATGTCACATTCGATTGGT
GGTGGCACAGGTAGTGGAATGGGAAGCCTTTTATTAAATAAACTCAAAGAAGAATATCAA
GATCGAGTTGTCAATACTTTTTCAGTTATTCCATCACCAAAAGTATCAGAAACTGTCGTT
GAACCTTACAATGCAATTTTGACACTTTCTGAAATGATCAATGATACTGATGAGACTGTT
TGCATTGATAATGAAGCATTATATGATATTTTTTATCATACATTAAAACTCTGTCATCCA
ACACTCGATGATCTTAATCATCTTATTGGTATGACAATGTCTGGTATAACAACTGGCTTT
CGCTATCCTGGACAATTGAATACAGATTTAAGAAAATTAATGACAAATATGTGTCCTTAT
CCACGACTACACTTCTTTATCCCGGGATTTGCTCCTCTCGCTACACGTGTCAGTGAAGCA
TACAGAAAAGTTACAACTTCTGACCTTGTTTGTCAAATTTTCGATTGTCGCAATCAAATG
GCCGCTTTTGATCCTCATTGTGGTCGATATCTTACATGTGCTGCAATATTTCGTGGTCTT
GTGTCATCACGTGAAATTGAACAACAATTGATGGCTATACAAGAACGAAATGCTGATTCA
TTTGCAAATTGGGTACCGAATAATATTAAAACAGCAATTTGTGATATTCCACCAAGAGGT
TTAAAATTATCAGCGACATTTATCTCAAATACGACAGCAATTCAAATTCTCTTTCGACGA
TTACTTGATCAATATCAGTCAATGTTTCAAAAGCGAGCTTTCATTCATTGGTATACTGGT
GAAGGAATGGAAGAGCATGAATTTAAAAGTGCTGAAGAAGGTGTGTTAGGAATAATTGAT
GAATATAATTGCTGTAATGAACAAGATCCAACTGATGATGAAATTTGTGAATTAGAAGAT
GAAAGTGCGACTGAGGAAGAAGAAGAATGCAATGAGAAATGTTAA

>g8705.t1 Gene=g8705 Length=454
MREIVSIQIGQCGNKIGEKFWEIISEEHNINRCGHFYGNSYLPYQRLGVYYETGPQEIFV
PRSILVDLDQASLNSVKCGLYGRIFNPDCFVVGRCGAGNNWARGHYTEGAELIESVLDVT
RKQVECCDCFQGFQMSHSIGGGTGSGMGSLLLNKLKEEYQDRVVNTFSVIPSPKVSETVV
EPYNAILTLSEMINDTDETVCIDNEALYDIFYHTLKLCHPTLDDLNHLIGMTMSGITTGF
RYPGQLNTDLRKLMTNMCPYPRLHFFIPGFAPLATRVSEAYRKVTTSDLVCQIFDCRNQM
AAFDPHCGRYLTCAAIFRGLVSSREIEQQLMAIQERNADSFANWVPNNIKTAICDIPPRG
LKLSATFISNTTAIQILFRRLLDQYQSMFQKRAFIHWYTGEGMEEHEFKSAEEGVLGIID
EYNCCNEQDPTDDEICELEDESATEEEEECNEKC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
30 g8705.t1 CDD cd02187 beta_tubulin 2 426 0.0
29 g8705.t1 Gene3D G3DSA:3.40.50.1440 - 1 263 4.6E-101
28 g8705.t1 Gene3D G3DSA:3.30.1330.20 - 264 373 1.1E-41
27 g8705.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 374 452 7.5E-20
3 g8705.t1 PANTHER PTHR11588 TUBULIN 1 436 4.4E-201
4 g8705.t1 PANTHER PTHR11588:SF293 TUBULIN BETA CHAIN-RELATED 1 436 4.4E-201
17 g8705.t1 PRINTS PR01161 Tubulin signature 10 30 8.3E-80
24 g8705.t1 PRINTS PR01161 Tubulin signature 51 70 8.3E-80
10 g8705.t1 PRINTS PR01163 Beta-tubulin signature 88 99 3.5E-62
20 g8705.t1 PRINTS PR01161 Tubulin signature 93 104 8.3E-80
21 g8705.t1 PRINTS PR01161 Tubulin signature 106 130 8.3E-80
12 g8705.t1 PRINTS PR01163 Beta-tubulin signature 108 126 3.5E-62
22 g8705.t1 PRINTS PR01161 Tubulin signature 132 150 8.3E-80
23 g8705.t1 PRINTS PR01161 Tubulin signature 151 172 8.3E-80
6 g8705.t1 PRINTS PR01163 Beta-tubulin signature 152 164 3.5E-62
19 g8705.t1 PRINTS PR01161 Tubulin signature 176 189 8.3E-80
18 g8705.t1 PRINTS PR01161 Tubulin signature 190 210 8.3E-80
15 g8705.t1 PRINTS PR01163 Beta-tubulin signature 212 224 3.5E-62
8 g8705.t1 PRINTS PR01163 Beta-tubulin signature 230 239 3.5E-62
7 g8705.t1 PRINTS PR01163 Beta-tubulin signature 245 258 3.5E-62
14 g8705.t1 PRINTS PR01163 Beta-tubulin signature 265 281 3.5E-62
9 g8705.t1 PRINTS PR01163 Beta-tubulin signature 311 329 3.5E-62
13 g8705.t1 PRINTS PR01163 Beta-tubulin signature 329 343 3.5E-62
5 g8705.t1 PRINTS PR01163 Beta-tubulin signature 347 370 3.5E-62
16 g8705.t1 PRINTS PR01161 Tubulin signature 370 398 8.3E-80
11 g8705.t1 PRINTS PR01163 Beta-tubulin signature 377 388 3.5E-62
1 g8705.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 210 1.9E-66
2 g8705.t1 Pfam PF03953 Tubulin C-terminal domain 261 382 4.6E-33
31 g8705.t1 ProSitePatterns PS00228 Tubulin-beta mRNA autoregulation signal. 1 4 -
32 g8705.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 140 146 -
33 g8705.t1 SMART SM00864 Tubulin_4 46 244 5.6E-50
34 g8705.t1 SMART SM00865 Tubulin_C_4 246 383 8.3E-25
25 g8705.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 243 1.01E-81
26 g8705.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 244 428 3.36E-66

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