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.t5 TSS g2687.t5 19716871 19716871
chr_3 g2687 g2687.t5 isoform g2687.t5 19716989 19718303
chr_3 g2687 g2687.t5 exon g2687.t5.exon1 19716989 19716991
chr_3 g2687 g2687.t5 cds g2687.t5.CDS1 19716989 19716991
chr_3 g2687 g2687.t5 exon g2687.t5.exon2 19717306 19717687
chr_3 g2687 g2687.t5 cds g2687.t5.CDS2 19717306 19717687
chr_3 g2687 g2687.t5 exon g2687.t5.exon3 19717856 19718303
chr_3 g2687 g2687.t5 cds g2687.t5.CDS3 19717856 19718301
chr_3 g2687 g2687.t5 TTS g2687.t5 19718842 19718842

Sequences

>g2687.t5 Gene=g2687 Length=833
ATGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGT
TGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAATGCCATCTGACAAG
ACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAACTGGTGCAGGCAAA
CACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCGATGAAGTCCGCACT
GGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGCTGCC
AACAACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCGATTTGGTTTTGGAT
CGCATCCGTAAATTGGCTGATCAATATAACTCAATCTTGACAACACATACAACTTTGGAA
CACTCTGACTGCGCATTCATGGTCGATAACGAAGCTATCTATGACATCTGCCGTCGTAAT
TTGGACATTGAACGCCCAACATATACCAACTTGAATCGTTTGATTGGCCAGATTGTCTCA
TCGATCACCGCATCACTCCGTTTCGATGGTGCATTGAACGTCGATTTGACTGAATTCCAA
ACTAACTTGGTACCATATCCACGTATTCACTTCCCATTGGTTACATATGCCCCAGTCATC
TCAGCTGAAAAAGCTTACCATGAACAATTGAGCGTTGCTGAAATCACAAACGCTTGTTTC
GAACCAGCCAACCAAATGGTCAAATGCGATCCACGTCATGGTAAATACATGGCTTGCTGC
ATGTTGTACAGAGGTGATGTTGTACCAAAAGATGTCAATGCAGCCATTGCTAC

>g2687.t5 Gene=g2687 Length=277
MRECISVHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIVDLVLD
RIRKLADQYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVS
SITASLRFDGALNVDLTEFQTNLVPYPRIHFPLVTYAPVISAEKAYHEQLSVAEITNACF
EPANQMVKCDPRHGKYMACCMLYRGDVVPKDVNAAIA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g2687.t5 CDD cd02186 alpha_tubulin 2 277 0
21 g2687.t5 Gene3D G3DSA:3.40.50.1440 - 1 127 0
20 g2687.t5 Gene3D G3DSA:3.40.50.1440 - 128 212 0
19 g2687.t5 Gene3D G3DSA:3.30.1330.20 - 213 277 0
3 g2687.t5 PANTHER PTHR11588:SF251 TUBULIN ALPHA-1B CHAIN 2 128 0
5 g2687.t5 PANTHER PTHR11588 TUBULIN 2 128 0
4 g2687.t5 PANTHER PTHR11588:SF251 TUBULIN ALPHA-1B CHAIN 128 277 0
6 g2687.t5 PANTHER PTHR11588 TUBULIN 128 277 0
14 g2687.t5 PRINTS PR01161 Tubulin signature 10 30 0
10 g2687.t5 PRINTS PR01162 Alpha-tubulin signature 18 33 0
9 g2687.t5 PRINTS PR01162 Alpha-tubulin signature 45 58 0
13 g2687.t5 PRINTS PR01161 Tubulin signature 53 72 0
7 g2687.t5 PRINTS PR01162 Alpha-tubulin signature 88 101 0
12 g2687.t5 PRINTS PR01161 Tubulin signature 95 106 0
11 g2687.t5 PRINTS PR01161 Tubulin signature 108 132 0
8 g2687.t5 PRINTS PR01162 Alpha-tubulin signature 120 128 0
1 g2687.t5 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 127 0
2 g2687.t5 Pfam PF03953 Tubulin C-terminal domain 207 276 0
17 g2687.t5 SMART SM00864 Tubulin_4 49 190 0
18 g2687.t5 SMART SM00865 Tubulin_C_4 192 277 0
15 g2687.t5 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 189 0
16 g2687.t5 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 190 276 0

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