Gene loci information

Transcript annotation

  • This transcript has been annotated as Tubulin gamma-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 g4425 g4425.t4 TSS g4425.t4 2115819 2115819
chr_2 g4425 g4425.t4 isoform g4425.t4 2115889 2117362
chr_2 g4425 g4425.t4 exon g4425.t4.exon1 2115889 2116763
chr_2 g4425 g4425.t4 cds g4425.t4.CDS1 2116232 2116763
chr_2 g4425 g4425.t4 exon g4425.t4.exon2 2116869 2117362
chr_2 g4425 g4425.t4 cds g4425.t4.CDS2 2116869 2117362
chr_2 g4425 g4425.t4 TTS g4425.t4 2117515 2117515

Sequences

>g4425.t4 Gene=g4425 Length=1369
ATGCCAAGTGAAATGATAACTTTACAATTAGGCCAATGTGGTAATCAAAGTAAGTTAAAT
ATTGTGCAATATTAAAACATTTGTTTAATAACTTGTGCTTTTTATTAGTTGGCTTCGAAT
TTTGGAAAAGATTATGTTTAGAGCATGGAATTTCTCCATCTGGTGTGCTTGAGGATTTTG
CAACTGATGGACCCGATAGAAAGGATGTCTTTTTTTATCAAGTAAATTTAAATTATTAAT
TATTTTTAAAATTATATAAAAAATAACATTTTAGGCTGATGATGATCACTACATTCCTAG
AGCTGTTTTGCTTGATTTAGAGCCTCGAGTAATTCATACAATAATGCAATCACAATATGC
AAAATTGTACAACCCAGAAAATATTTATCTTTCAAAAGATGGTGGTGGTGCTGGAAATAA
TTGGGCAAGTGGATTTAGTCAAGGAGAAAAGTTGCAAGAGGAAGTTTTTGATATTATCGA
CAGAGAGGCAGATGGAAGCGATAGTTTAGAAGGCTTTGTTTTATGCCATTCAATTGCTGG
TGGAACAGGTAGTGGAATGGGAAGTTATATAATGGAAAGATTGTCTGATCATTTTCCTAA
GAAACTTGTGCAAACGTATAGTGTTTTTCCGAATCAAGATGAAATTAGTGATGTTGTTGT
GCAACCGTATAACTCATTGTTGACTTTGAGGCGATTAACAAGCTGTGCAGATTGTGTTGT
GGTTTTGGACAATACAGCTCTTAATCGTATTGCAACTGATAGATTGCATATTGAAAATCC
TTCATTCACTCAAATCAATACTCTGGTTTCAACAATCATGTCAGTTAGCACAACTACTTT
ACGCTACCCTTCATACATGAATAATAATCTGATTGTTTTAGATGTAATGAGAAGATTGCT
TCAACCAAAAAATATGATGGTCTCAACAGGTCCAGATAAAACAAATCATCATTGCTATAT
CTCAATATTAAATATTATTCAAGGAGAAGTTGATCCAACGCAAGTACATAAATCTCTTCA
ACGTATTCGAGAGAGAAAACTTGCTCAATTTATTCCTTGGGGTCCTGCATCAATTCAAGT
AGCTCTCTCGAGAAGTTCTCCTTATGTTCAAAGTAGTCATCGTGTATCAGGACTCATGCT
TGCTAATCATACCAGTATTTGTTCATTATTTGAAAGAGCTTTAAATCAATACGATAAATT
GCGCAAACGTGGAGCTTTTTTGGATCAGTTCCGCAAAGAAGAAATGTTTAAAGATGATTT
ACATGAATTGGATGATTCACGAGATATTGTTGATTCACTCGTACAAGAATACGAAGCTGC
AACTCGACATGATTATTTACAATGGCAAGCTAAAAAGGATATTGAATAA

>g4425.t4 Gene=g4425 Length=341
MQSQYAKLYNPENIYLSKDGGGAGNNWASGFSQGEKLQEEVFDIIDREADGSDSLEGFVL
CHSIAGGTGSGMGSYIMERLSDHFPKKLVQTYSVFPNQDEISDVVVQPYNSLLTLRRLTS
CADCVVVLDNTALNRIATDRLHIENPSFTQINTLVSTIMSVSTTTLRYPSYMNNNLIVLD
VMRRLLQPKNMMVSTGPDKTNHHCYISILNIIQGEVDPTQVHKSLQRIRERKLAQFIPWG
PASIQVALSRSSPYVQSSHRVSGLMLANHTSICSLFERALNQYDKLRKRGAFLDQFRKEE
MFKDDLHELDDSRDIVDSLVQEYEAATRHDYLQWQAKKDIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g4425.t4 CDD cd02188 gamma_tubulin 1 323 0.0
19 g4425.t4 Gene3D G3DSA:3.40.50.1440 - 1 270 1.3E-83
18 g4425.t4 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 271 330 6.3E-24
3 g4425.t4 PANTHER PTHR11588:SF79 TUBULIN GAMMA-2 CHAIN 2 179 2.9E-180
5 g4425.t4 PANTHER PTHR11588 TUBULIN 2 179 2.9E-180
4 g4425.t4 PANTHER PTHR11588:SF79 TUBULIN GAMMA-2 CHAIN 177 330 2.9E-180
6 g4425.t4 PANTHER PTHR11588 TUBULIN 177 330 2.9E-180
15 g4425.t4 PRINTS PR01161 Tubulin signature 19 30 3.4E-44
14 g4425.t4 PRINTS PR01161 Tubulin signature 31 55 3.4E-44
7 g4425.t4 PRINTS PR01164 Gamma-tubulin signature 39 54 2.0E-13
12 g4425.t4 PRINTS PR01161 Tubulin signature 57 75 3.4E-44
13 g4425.t4 PRINTS PR01161 Tubulin signature 76 97 3.4E-44
9 g4425.t4 PRINTS PR01161 Tubulin signature 102 115 3.4E-44
10 g4425.t4 PRINTS PR01161 Tubulin signature 116 136 3.4E-44
11 g4425.t4 PRINTS PR01161 Tubulin signature 268 296 3.4E-44
8 g4425.t4 PRINTS PR01164 Gamma-tubulin signature 308 331 2.0E-13
1 g4425.t4 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 4 137 1.5E-41
2 g4425.t4 Pfam PF03953 Tubulin C-terminal domain 174 280 4.2E-38
21 g4425.t4 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 65 71 -
22 g4425.t4 SMART SM00864 Tubulin_4 1 170 3.5E-36
23 g4425.t4 SMART SM00865 Tubulin_C_4 151 281 6.8E-9
16 g4425.t4 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 3 169 8.63E-54
17 g4425.t4 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 171 330 1.13E-46

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:0000930 gamma-tubulin complex CC
GO:0005874 microtubule CC
GO:0007017 microtubule-based process BP
GO:0005525 GTP binding MF
GO:0031122 cytoplasmic microtubule organization BP
GO:0007020 microtubule nucleation BP
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