Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin alpha chain, testis-specific.

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.t12 TSS g2687.t12 19716871 19716871
chr_3 g2687 g2687.t12 isoform g2687.t12 19716989 19718655
chr_3 g2687 g2687.t12 exon g2687.t12.exon1 19716989 19716991
chr_3 g2687 g2687.t12 cds g2687.t12.CDS1 19716989 19716991
chr_3 g2687 g2687.t12 exon g2687.t12.exon2 19717306 19717631
chr_3 g2687 g2687.t12 cds g2687.t12.CDS2 19717306 19717631
chr_3 g2687 g2687.t12 exon g2687.t12.exon3 19718319 19718655
chr_3 g2687 g2687.t12 cds g2687.t12.CDS3 19718319 19718655
chr_3 g2687 g2687.t12 TTS g2687.t12 19718842 19718842

Sequences

>g2687.t12 Gene=g2687 Length=666
ATGCGTGAATGTATCTCAGTTCATGTTGGTCAAGCTGGTGTCCAAATCGGAAATGCCTGT
TGGGAACTTTACTGTCTTGAACACGGTATTCAGCCAGATGGTCAAATGCCATCTGACAAG
ACAATTGGTGGAGGGGATGACTCATTCAACACTTTCTTCTCGGAAACTGGTGCAGGCAAA
CACGTTCCACGTGCTGTTTTTGTTGATTTGGAACCAACTGTCGTCGATGAAGTCCGCACT
GGAACTTATCGTCAACTTTTCCATCCTGAACAATTGATCACTGGTAAGGAAGATGCTGCC
AACAACTACGCTCGTGGACACTACACTATTACCATTCAATTTGTCGATTGGTGTCCAACT
GGTTTCAAAGTTGGTATCAATTATCAACCACCAACTGTTGTTCCAGGCGGTGATTTGGCC
AAGGTTCAACGCGCTGTTTGCATGTTGTCAAACACAACTGCCATCGCTGAAGCATGGGCT
CGTCTTGATCATAAATTCGATTTGATGTATGCCAAGCGTGCATTCGTTCACTGGTATGTC
GGTGAAGGTATGGAAGAAGGTGAATTCTCAGAAGCTCGTGAGGATTTGGCCGCTTTGGAG
AAAGATTATGAAGAAGTTGGCATGGACTCTGGCGAGGGAGAAGGCGAAGGCGCAGAAGAA
TACTAA

>g2687.t12 Gene=g2687 Length=221
MRECISVHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTITIQFVDWCPT
GFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYV
GEGMEEGEFSEAREDLAALEKDYEEVGMDSGEGEGEGAEEY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g2687.t12 Coils Coil Coil 189 209 -
16 g2687.t12 Gene3D G3DSA:3.40.50.1440 - 1 121 2.5E-53
15 g2687.t12 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 155 208 2.1E-34
3 g2687.t12 PANTHER PTHR11588:SF390 TUBULIN ALPHA CHAIN 2 110 1.0E-138
5 g2687.t12 PANTHER PTHR11588 TUBULIN 2 110 1.0E-138
4 g2687.t12 PANTHER PTHR11588:SF390 TUBULIN ALPHA CHAIN 111 216 1.0E-138
6 g2687.t12 PANTHER PTHR11588 TUBULIN 111 216 1.0E-138
12 g2687.t12 PRINTS PR01161 Tubulin signature 10 30 4.8E-24
9 g2687.t12 PRINTS PR01162 Alpha-tubulin signature 18 33 1.1E-22
8 g2687.t12 PRINTS PR01162 Alpha-tubulin signature 45 58 1.1E-22
11 g2687.t12 PRINTS PR01161 Tubulin signature 53 72 4.8E-24
7 g2687.t12 PRINTS PR01162 Alpha-tubulin signature 88 101 1.1E-22
10 g2687.t12 PRINTS PR01161 Tubulin signature 95 106 4.8E-24
1 g2687.t12 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 3 113 7.2E-30
2 g2687.t12 Pfam PF03953 Tubulin C-terminal domain 105 163 2.3E-15
13 g2687.t12 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 1 116 6.54E-43
14 g2687.t12 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 108 208 1.89E-43

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