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.t2 TSS g4425.t2 2115819 2115819
chr_2 g4425 g4425.t2 isoform g4425.t2 2115889 2117362
chr_2 g4425 g4425.t2 exon g4425.t2.exon1 2115889 2117238
chr_2 g4425 g4425.t2 cds g4425.t2.CDS1 2116232 2117238
chr_2 g4425 g4425.t2 exon g4425.t2.exon2 2117316 2117362
chr_2 g4425 g4425.t2 cds g4425.t2.CDS2 2117316 2117325
chr_2 g4425 g4425.t2 TTS g4425.t2 2117515 2117515

Sequences

>g4425.t2 Gene=g4425 Length=1397
ATGCCAAGTGAAATGATAACTTTACAATTAGGCCAATGTGGTAATCAAAGTAAGTTAAAT
ATTGTGCAATATTAAAACATTTGTTTAATAACTTGTGCTTTTTATTAGTTGGCTTCGAAT
TTTGGAAAAGATTATGTTTAGAGCATGGAATTTCTCCATCTGGTGTGCTTGAGGATTTTG
CAACTGATGGACCCGATAGAAAGGATGTCTTTTTTTATCAAGTAAATTTAAATTATTAAT
TATTTTTAAAATTATATAAAAAATAACATTTTAGGCTGATGATGATCACTACATTCCTAG
AGCTGTTTTGCTTGATTTAGAGCCTCGAGTAATTCATACAATAATGCAATCACAATATGC
AAAATTGTACAACCCAGAAAATATTTATCTTTCAAAAGATGGTGGTGGTGCTGGAAATAA
TTGGGCAAGTGGATTTAGTCAAGGAGAAAAGTTGCAAGAGGAAGTTTTTGATATTATCGA
CAGAGAGGCAGATGGAAGCGATAGTTTAGAAGGCTTTGTTTTATGCCATTCAATTGCTGG
TGGAACAGGTAGTGGAATGGGAAGTTATATAATGGAAAGATTGTCTGATCATTTTCCTAA
GAAACTTGTGCAAACGTATAGTGTTTTTCCGAATCAAGATGAAATTAGTGATGTTGTTGT
GCAACCGTATAACTCATTGTTGACTTTGAGGCGATTAACAAGCTGTGCAGATTGTGTTGT
GGTTTTGGACAATACAGCTCTTAATCGTATTGCAACTGATAGATTGCATATTGAAAATCC
TTCATTCACTCAAATCAATACTCTGGTTTCAACAATCATGTCAGTTAGCACAACTACTTT
ACGCTACCCTTCATACATGAATAATAATCTGATTGGTTTAACAGCACCTCTTATTCCAAC
GCCACAACTTCATTTTCTCATGACTGGCTATACTCCACTCACTACTGAAACTGATATATC
AAACGTTCGGAAAACTACAGTTTTAGATGTAATGAGAAGATTGCTTCAACCAAAAAATAT
GATGGTCTCAACAGGTCCAGATAAAACAAATCATCATTGCTATATCTCAATATTAAATAT
TATTCAAGGAGAAGTTGATCCAACGCAAGTACATAAATCTCTTCAACGTATTCGAGAGAG
AAAACTTGCTCAATTTATTCCTTGGGGTCCTGCATCAATTCAAGTAGCTCTCTCGAGAAG
TTCTCCTTATGTTCAAAGTAGTCATCGTGTATCAGGACTCATGCTTGCTAATCATACCAG
TATTTGTTCATTATTTGAAAGAGCTTTAAATCAATACGATAAATTGCGCAAACGTGGAGC
TTTTTTGGATCAGTTCCGCAAAGAAGAAATCTCGACATGATTATTTACAATGGCAAGCTA
AAAAGGATATTGAATAA

>g4425.t2 Gene=g4425 Length=338
MQSQYAKLYNPENIYLSKDGGGAGNNWASGFSQGEKLQEEVFDIIDREADGSDSLEGFVL
CHSIAGGTGSGMGSYIMERLSDHFPKKLVQTYSVFPNQDEISDVVVQPYNSLLTLRRLTS
CADCVVVLDNTALNRIATDRLHIENPSFTQINTLVSTIMSVSTTTLRYPSYMNNNLIGLT
APLIPTPQLHFLMTGYTPLTTETDISNVRKTTVLDVMRRLLQPKNMMVSTGPDKTNHHCY
ISILNIIQGEVDPTQVHKSLQRIRERKLAQFIPWGPASIQVALSRSSPYVQSSHRVSGLM
LANHTSICSLFERALNQYDKLRKRGAFLDQFRKEEIST

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g4425.t2 CDD cd02188 gamma_tubulin 1 337 0.0
22 g4425.t2 Gene3D G3DSA:3.40.50.1440 - 1 192 1.0E-68
21 g4425.t2 Gene3D G3DSA:3.30.1330.20 - 193 304 1.1E-55
20 g4425.t2 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 305 338 4.4E-11
3 g4425.t2 PANTHER PTHR11588:SF79 TUBULIN GAMMA-2 CHAIN 2 336 6.6E-200
4 g4425.t2 PANTHER PTHR11588 TUBULIN 2 336 6.6E-200
17 g4425.t2 PRINTS PR01161 Tubulin signature 19 30 3.2E-44
16 g4425.t2 PRINTS PR01161 Tubulin signature 31 55 3.2E-44
7 g4425.t2 PRINTS PR01164 Gamma-tubulin signature 39 54 3.9E-56
13 g4425.t2 PRINTS PR01161 Tubulin signature 57 75 3.2E-44
15 g4425.t2 PRINTS PR01161 Tubulin signature 76 97 3.2E-44
11 g4425.t2 PRINTS PR01161 Tubulin signature 102 115 3.2E-44
6 g4425.t2 PRINTS PR01164 Gamma-tubulin signature 116 129 3.9E-56
12 g4425.t2 PRINTS PR01161 Tubulin signature 116 136 3.2E-44
10 g4425.t2 PRINTS PR01164 Gamma-tubulin signature 174 185 3.9E-56
8 g4425.t2 PRINTS PR01164 Gamma-tubulin signature 209 224 3.9E-56
9 g4425.t2 PRINTS PR01164 Gamma-tubulin signature 262 285 3.9E-56
5 g4425.t2 PRINTS PR01164 Gamma-tubulin signature 287 307 3.9E-56
14 g4425.t2 PRINTS PR01161 Tubulin signature 303 331 3.2E-44
1 g4425.t2 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 4 137 1.4E-41
2 g4425.t2 Pfam PF03953 Tubulin C-terminal domain 187 315 5.6E-49
24 g4425.t2 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 65 71 -
25 g4425.t2 SMART SM00864 Tubulin_4 1 170 3.5E-36
26 g4425.t2 SMART SM00865 Tubulin_C_4 172 316 2.7E-27
18 g4425.t2 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 3 169 8.37E-54
19 g4425.t2 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 170 336 2.56E-55

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