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.t3 TSS g4425.t3 2115819 2115819
chr_2 g4425 g4425.t3 isoform g4425.t3 2115889 2117362
chr_2 g4425 g4425.t3 exon g4425.t3.exon1 2115889 2116109
chr_2 g4425 g4425.t3 exon g4425.t3.exon2 2116163 2117362
chr_2 g4425 g4425.t3 cds g4425.t3.CDS1 2116232 2117362
chr_2 g4425 g4425.t3 TTS g4425.t3 2117515 2117515

Sequences

>g4425.t3 Gene=g4425 Length=1421
ATGCCAAGTGAAATGATAACTTTACAATTAGGCCAATGTGGTAATCAAAGTAAGTTAAAT
ATTGTGCAATATTAAAACATTTGTTTAATAACTTGTGCTTTTTATTAGTTGGCTTCGAAT
TTTGGAAAAGATTATGTTTAGAGCATGGAATTTCTCCATCTGGTGTGCTTGAGGATTTTG
CAACTGATGGACCCGATAGAAAGGATGTCTTTTTTTATCAAGCTGATGATGATCACTACA
TTCCTAGAGCTGTTTTGCTTGATTTAGAGCCTCGAGTAATTCATACAATAATGCAATCAC
AATATGCAAAATTGTACAACCCAGAAAATATTTATCTTTCAAAAGATGGTGGTGGTGCTG
GAAATAATTGGGCAAGTGGATTTAGTCAAGGAGAAAAGTTGCAAGAGGAAGTTTTTGATA
TTATCGACAGAGAGGCAGATGGAAGCGATAGTTTAGAAGGCTTTGTTTTATGCCATTCAA
TTGCTGGTGGAACAGGTAGTGGAATGGGAAGTTATATAATGGAAAGATTGTCTGATCATT
TTCCTAAGAAACTTGTGCAAACGTATAGTGTTTTTCCGAATCAAGATGAAATTAGTGATG
TTGTTGTGCAACCGTATAACTCATTGTTGACTTTGAGGCGATTAACAAGCTGTGCAGATT
GTGTTGTGGTTTTGGACAATACAGCTCTTAATCGTATTGCAACTGATAGATTGCATATTG
AAAATCCTTCATTCACTCAAATCAATACTCTGGTTTCAACAATCATGTCAGTTAGCACAA
CTACTTTACGCTACCCTTCATACATGAATAATAATCTGATTGGTTTAACAGCACCTCTTA
TTCCAACGCCACAACTTCATTTTCTCATGACTGGCTATACTCCACTCACTACTGAAACTG
ATATATCAAACGTTCGGAAAACTACAGTTTTAGATGTAATGAGAAGATTGCTTCAACCAA
AAAATATGATGGTCTCAACAGGTCCAGATAAAACAAATCATCATTGCTATATCTCAATAT
TAAATATTATTCAAGGAGAAGTTGATCCAACGCAAGTACATAAATCTCTTCAACGTATTC
GAGAGAGAAAACTTGCTCAATTTATTCCTTGGGGTCCTGCATCAATTCAAGTAGCTCTCT
CGAGAAGTTCTCCTTATGTTCAAAGTAGTCATCGTGTATCAGGACTCATGCTTGCTAATC
ATACCAGTATTTGTTCATTATTTGAAAGAGCTTTAAATCAATACGATAAATTGCGCAAAC
GTGGAGCTTTTTTGGATCAGTTCCGCAAAGAAGAAATGTTTAAAGATGATTTACATGAAT
TGGATGATTCACGAGATATTGTTGATTCACTCGTACAAGAATACGAAGCTGCAACTCGAC
ATGATTATTTACAATGGCAAGCTAAAAAGGATATTGAATAA

>g4425.t3 Gene=g4425 Length=376
MQSQYAKLYNPENIYLSKDGGGAGNNWASGFSQGEKLQEEVFDIIDREADGSDSLEGFVL
CHSIAGGTGSGMGSYIMERLSDHFPKKLVQTYSVFPNQDEISDVVVQPYNSLLTLRRLTS
CADCVVVLDNTALNRIATDRLHIENPSFTQINTLVSTIMSVSTTTLRYPSYMNNNLIGLT
APLIPTPQLHFLMTGYTPLTTETDISNVRKTTVLDVMRRLLQPKNMMVSTGPDKTNHHCY
ISILNIIQGEVDPTQVHKSLQRIRERKLAQFIPWGPASIQVALSRSSPYVQSSHRVSGLM
LANHTSICSLFERALNQYDKLRKRGAFLDQFRKEEMFKDDLHELDDSRDIVDSLVQEYEA
ATRHDYLQWQAKKDIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g4425.t3 CDD cd02188 gamma_tubulin 1 358 0.0
24 g4425.t3 Coils Coil Coil 373 376 -
23 g4425.t3 Gene3D G3DSA:3.40.50.1440 - 1 192 1.3E-68
22 g4425.t3 Gene3D G3DSA:3.30.1330.20 - 193 304 1.4E-55
21 g4425.t3 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 305 365 7.4E-24
3 g4425.t3 PANTHER PTHR11588:SF79 TUBULIN GAMMA-2 CHAIN 2 365 2.0E-207
4 g4425.t3 PANTHER PTHR11588 TUBULIN 2 365 2.0E-207
18 g4425.t3 PRINTS PR01161 Tubulin signature 19 30 5.9E-44
17 g4425.t3 PRINTS PR01161 Tubulin signature 31 55 5.9E-44
7 g4425.t3 PRINTS PR01164 Gamma-tubulin signature 39 54 3.2E-66
14 g4425.t3 PRINTS PR01161 Tubulin signature 57 75 5.9E-44
16 g4425.t3 PRINTS PR01161 Tubulin signature 76 97 5.9E-44
12 g4425.t3 PRINTS PR01161 Tubulin signature 102 115 5.9E-44
6 g4425.t3 PRINTS PR01164 Gamma-tubulin signature 116 129 3.2E-66
13 g4425.t3 PRINTS PR01161 Tubulin signature 116 136 5.9E-44
10 g4425.t3 PRINTS PR01164 Gamma-tubulin signature 174 185 3.2E-66
8 g4425.t3 PRINTS PR01164 Gamma-tubulin signature 209 224 3.2E-66
9 g4425.t3 PRINTS PR01164 Gamma-tubulin signature 262 285 3.2E-66
5 g4425.t3 PRINTS PR01164 Gamma-tubulin signature 287 307 3.2E-66
15 g4425.t3 PRINTS PR01161 Tubulin signature 303 331 5.9E-44
11 g4425.t3 PRINTS PR01164 Gamma-tubulin signature 343 366 3.2E-66
1 g4425.t3 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 4 137 1.8E-41
2 g4425.t3 Pfam PF03953 Tubulin C-terminal domain 187 315 7.0E-49
26 g4425.t3 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 65 71 -
27 g4425.t3 SMART SM00864 Tubulin_4 1 170 3.5E-36
28 g4425.t3 SMART SM00865 Tubulin_C_4 172 316 2.7E-27
19 g4425.t3 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 3 169 1.09E-53
20 g4425.t3 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 170 365 1.13E-61

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.

Raw TPM values