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.t8 TSS g2687.t8 19716871 19716871
chr_3 g2687 g2687.t8 isoform g2687.t8 19716989 19718655
chr_3 g2687 g2687.t8 exon g2687.t8.exon1 19716989 19716991
chr_3 g2687 g2687.t8 exon g2687.t8.exon2 19717306 19717375
chr_3 g2687 g2687.t8 cds g2687.t8.CDS1 19717355 19717375
chr_3 g2687 g2687.t8 exon g2687.t8.exon3 19717951 19718655
chr_3 g2687 g2687.t8 cds g2687.t8.CDS2 19717951 19718655
chr_3 g2687 g2687.t8 TTS g2687.t8 19718842 19718842

Sequences

>g2687.t8 Gene=g2687 Length=778
ATGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGT
TGGGAACTTTACTTTGGACATTGAACGCCCAACATATACCAACTTGAATCGTTTGATTGG
CCAGATTGTCTCATCGATCACCGCATCACTCCGTTTCGATGGTGCATTGAACGTCGATTT
GACTGAATTCCAAACTAACTTGGTACCATATCCACGTATTCACTTCCCATTGGTTACATA
TGCCCCAGTCATCTCAGCTGAAAAAGCTTACCATGAACAATTGAGCGTTGCTGAAATCAC
AAACGCTTGTTTCGAACCAGCCAACCAAATGGTCAAATGCGATCCACGTCATGGTAAATA
CATGGCTTGCTGCATGTTGTACAGAGGTGATGTTGTACCAAAAGATGTCAATGCAGCCAT
TGCTACAATCAAGACAAAACGTACCATTCAATTTGTCGATTGGTGTCCAACTGGTTTCAA
AGTTGGTATCAATTATCAACCACCAACTGTTGTTCCAGGCGGTGATTTGGCCAAGGTTCA
ACGCGCTGTTTGCATGTTGTCAAACACAACTGCCATCGCTGAAGCATGGGCTCGTCTTGA
TCATAAATTCGATTTGATGTATGCCAAGCGTGCATTCGTTCACTGGTATGTCGGTGAAGG
TATGGAAGAAGGTGAATTCTCAGAAGCTCGTGAGGATTTGGCCGCTTTGGAGAAAGATTA
TGAAGAAGTTGGCATGGACTCTGGCGAGGGAGAAGGCGAAGGCGCAGAAGAATACTAA

>g2687.t8 Gene=g2687 Length=241
MPVGNFTLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPL
VTYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCMLYRGDVVPKDVN
AAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWA
RLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGMDSGEGEGEGAEE
Y

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g2687.t8 Coils Coil Coil 209 229 -
15 g2687.t8 Gene3D G3DSA:3.40.50.1440 - 3 59 3.0E-18
14 g2687.t8 Gene3D G3DSA:3.30.1330.20 - 60 174 1.8E-68
13 g2687.t8 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 175 228 2.4E-34
2 g2687.t8 PANTHER PTHR11588:SF366 TUBULIN ALPHA-3 CHAIN 7 238 2.0E-165
3 g2687.t8 PANTHER PTHR11588 TUBULIN 7 238 2.0E-165
9 g2687.t8 PRINTS PR01162 Alpha-tubulin signature 5 17 1.6E-72
7 g2687.t8 PRINTS PR01162 Alpha-tubulin signature 65 80 1.6E-72
10 g2687.t8 PRINTS PR01162 Alpha-tubulin signature 112 133 1.6E-72
6 g2687.t8 PRINTS PR01162 Alpha-tubulin signature 138 151 1.6E-72
5 g2687.t8 PRINTS PR01162 Alpha-tubulin signature 151 170 1.6E-72
8 g2687.t8 PRINTS PR01162 Alpha-tubulin signature 176 192 1.6E-72
4 g2687.t8 PRINTS PR01162 Alpha-tubulin signature 213 229 1.6E-72
1 g2687.t8 Pfam PF03953 Tubulin C-terminal domain 54 183 1.6E-53
12 g2687.t8 SMART SM00865 Tubulin_C_4 39 184 1.2E-60
11 g2687.t8 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 37 228 3.36E-88

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

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