Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin alpha-3 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.t14 TSS g2687.t14 19716871 19716871
chr_3 g2687 g2687.t14 isoform g2687.t14 19716989 19718655
chr_3 g2687 g2687.t14 exon g2687.t14.exon1 19716989 19717914
chr_3 g2687 g2687.t14 exon g2687.t14.exon2 19717980 19718655
chr_3 g2687 g2687.t14 cds g2687.t14.CDS1 19718206 19718655
chr_3 g2687 g2687.t14 TTS g2687.t14 19718842 19718842

Sequences

>g2687.t14 Gene=g2687 Length=1602
ATGGTAAGTAACATAATTATCAAATAAAATTCTTGATAAATAAGTGTGAAAAATCTAAAA
ACATTTTGTTCAGTCCGTTAGGACGCCATTTTAGTTTTTTTCTGCTTAAAGTACTATAAA
TTTTAATGCATAAACTAATTTATCCTTTTCCTATCAAGTTAAATATTATATTGATAAACT
TTCTTACTAGATTTTTTTTCATTTATGCTATTTTCATACCACGCCCAATTTTCTTAACCA
AATCGATATTTTTTTATGATTTTTATGCTGATGACTCATCCAATTTTTTTCAATTTCTTT
CTCATTAAATACTATAGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAA
TCGGAAATGCCTGTTGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAA
TGCCATCTGACAAGACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAA
CTGGTGCAGGCAAACACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCG
ATGAAGTCCGCACTGGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTA
AGGAAGATGCTGCCAACAACTACGCTCGTGGACACTACACTATTGGAAAGGAAATTGTCG
ATTTGGTTTTGGATCGCATCCGTAAATTGGCTGATCAATGTACTGGATTGCAAGGATTCT
TAATTTTCCACTCATTCGGTGGCGGTACTGGATCAGGCTTCACATCACTTTTGATGGAAC
GTCTCTCAGTTGATTATGGCAAGAAATCAAAATTGGAATTCGCAATCTATCCAGCACCAC
AAGTATCTACTGCTGTTGTTGAACCATATAACTCAATCTTGACAACACATACAACTTTGG
AACACTCTGACTGCGCATTCATGGTCCTTGAATCGTTTGATTGGCCAGATTGTCTCATCG
ATCACCGCATCACTCCGTTTCGATGGTGCATTGAACGTCGATTTGACTGAATTCCAAACT
AACTTGGTACCATATCCACGTATTCACTTCCCATTGGTTACATATGCCCCAGTCATCTCA
GCTGAAAAAGCTTACCATGAACAATTGAGCGTTGCTGAAATCACAAACGCTTGTTTCGAA
CCAGCCAACCAAATGGTCAAATGCGATCCACGTCATGGTAAATACATGGCTTGCTGCATG
TTGTACAGAGGTGATGTTGTACCAAAAGATGTCAATGCAGCCATTGCTACAATCAAGACA
AAACGTACCATTCAATTTGTCGATTGGTGTCCAACTGGTTTCAAAGTTGGTATCAATTAT
CAACCACCAACTGTTGTTCCAGGCGGTGATTTGGCCAAGGTTCAACGCGCTGTTTGCATG
TTGTCAAACACAACTGCCATCGCTGAAGCATGGGCTCGTCTTGATCATAAATTCGATTTG
ATGTATGCCAAGCGTGCATTCGTTCACTGGTATGTCGGTGAAGGTATGGAAGAAGGTGAA
TTCTCAGAAGCTCGTGAGGATTTGGCCGCTTTGGAGAAAGATTATGAAGAAGTTGGCATG
GACTCTGGCGAGGGAGAAGGCGAAGGCGCAGAAGAATACTAA

>g2687.t14 Gene=g2687 Length=149
MVKCDPRHGKYMACCMLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPPT
VVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEA
REDLAALEKDYEEVGMDSGEGEGEGAEEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2687.t14 Coils Coil Coil 117 137 -
12 g2687.t14 Gene3D G3DSA:3.30.1330.20 - 1 82 2.8E-49
11 g2687.t14 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 83 136 9.8E-35
2 g2687.t14 PANTHER PTHR11588:SF390 TUBULIN ALPHA CHAIN 1 144 5.8E-102
3 g2687.t14 PANTHER PTHR11588 TUBULIN 1 144 5.8E-102
4 g2687.t14 PRINTS PR01162 Alpha-tubulin signature 20 41 3.4E-57
7 g2687.t14 PRINTS PR01162 Alpha-tubulin signature 46 59 3.4E-57
6 g2687.t14 PRINTS PR01162 Alpha-tubulin signature 59 78 3.4E-57
5 g2687.t14 PRINTS PR01162 Alpha-tubulin signature 84 100 3.4E-57
8 g2687.t14 PRINTS PR01162 Alpha-tubulin signature 121 137 3.4E-57
1 g2687.t14 Pfam PF03953 Tubulin C-terminal domain 1 91 7.3E-35
10 g2687.t14 SMART SM00865 Tubulin_C_4 1 92 5.7E-9
9 g2687.t14 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 1 136 3.97E-63

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