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.t1 TSS g4425.t1 2115819 2115819
chr_2 g4425 g4425.t1 isoform g4425.t1 2115889 2117362
chr_2 g4425 g4425.t1 exon g4425.t1.exon1 2115889 2115937
chr_2 g4425 g4425.t1 cds g4425.t1.CDS1 2115889 2115937
chr_2 g4425 g4425.t1 exon g4425.t1.exon2 2115997 2116109
chr_2 g4425 g4425.t1 cds g4425.t1.CDS2 2115997 2116109
chr_2 g4425 g4425.t1 exon g4425.t1.exon3 2116163 2117362
chr_2 g4425 g4425.t1 cds g4425.t1.CDS3 2116163 2117362
chr_2 g4425 g4425.t1 TTS g4425.t1 2117515 2117515

Sequences

>g4425.t1 Gene=g4425 Length=1362
ATGCCAAGTGAAATGATAACTTTACAATTAGGCCAATGTGGTAATCAAATTGGCTTCGAA
TTTTGGAAAAGATTATGTTTAGAGCATGGAATTTCTCCATCTGGTGTGCTTGAGGATTTT
GCAACTGATGGACCCGATAGAAAGGATGTCTTTTTTTATCAAGCTGATGATGATCACTAC
ATTCCTAGAGCTGTTTTGCTTGATTTAGAGCCTCGAGTAATTCATACAATAATGCAATCA
CAATATGCAAAATTGTACAACCCAGAAAATATTTATCTTTCAAAAGATGGTGGTGGTGCT
GGAAATAATTGGGCAAGTGGATTTAGTCAAGGAGAAAAGTTGCAAGAGGAAGTTTTTGAT
ATTATCGACAGAGAGGCAGATGGAAGCGATAGTTTAGAAGGCTTTGTTTTATGCCATTCA
ATTGCTGGTGGAACAGGTAGTGGAATGGGAAGTTATATAATGGAAAGATTGTCTGATCAT
TTTCCTAAGAAACTTGTGCAAACGTATAGTGTTTTTCCGAATCAAGATGAAATTAGTGAT
GTTGTTGTGCAACCGTATAACTCATTGTTGACTTTGAGGCGATTAACAAGCTGTGCAGAT
TGTGTTGTGGTTTTGGACAATACAGCTCTTAATCGTATTGCAACTGATAGATTGCATATT
GAAAATCCTTCATTCACTCAAATCAATACTCTGGTTTCAACAATCATGTCAGTTAGCACA
ACTACTTTACGCTACCCTTCATACATGAATAATAATCTGATTGGTTTAACAGCACCTCTT
ATTCCAACGCCACAACTTCATTTTCTCATGACTGGCTATACTCCACTCACTACTGAAACT
GATATATCAAACGTTCGGAAAACTACAGTTTTAGATGTAATGAGAAGATTGCTTCAACCA
AAAAATATGATGGTCTCAACAGGTCCAGATAAAACAAATCATCATTGCTATATCTCAATA
TTAAATATTATTCAAGGAGAAGTTGATCCAACGCAAGTACATAAATCTCTTCAACGTATT
CGAGAGAGAAAACTTGCTCAATTTATTCCTTGGGGTCCTGCATCAATTCAAGTAGCTCTC
TCGAGAAGTTCTCCTTATGTTCAAAGTAGTCATCGTGTATCAGGACTCATGCTTGCTAAT
CATACCAGTATTTGTTCATTATTTGAAAGAGCTTTAAATCAATACGATAAATTGCGCAAA
CGTGGAGCTTTTTTGGATCAGTTCCGCAAAGAAGAAATGTTTAAAGATGATTTACATGAA
TTGGATGATTCACGAGATATTGTTGATTCACTCGTACAAGAATACGAAGCTGCAACTCGA
CATGATTATTTACAATGGCAAGCTAAAAAGGATATTGAATAA

>g4425.t1 Gene=g4425 Length=453
MPSEMITLQLGQCGNQIGFEFWKRLCLEHGISPSGVLEDFATDGPDRKDVFFYQADDDHY
IPRAVLLDLEPRVIHTIMQSQYAKLYNPENIYLSKDGGGAGNNWASGFSQGEKLQEEVFD
IIDREADGSDSLEGFVLCHSIAGGTGSGMGSYIMERLSDHFPKKLVQTYSVFPNQDEISD
VVVQPYNSLLTLRRLTSCADCVVVLDNTALNRIATDRLHIENPSFTQINTLVSTIMSVST
TTLRYPSYMNNNLIGLTAPLIPTPQLHFLMTGYTPLTTETDISNVRKTTVLDVMRRLLQP
KNMMVSTGPDKTNHHCYISILNIIQGEVDPTQVHKSLQRIRERKLAQFIPWGPASIQVAL
SRSSPYVQSSHRVSGLMLANHTSICSLFERALNQYDKLRKRGAFLDQFRKEEMFKDDLHE
LDDSRDIVDSLVQEYEAATRHDYLQWQAKKDIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
27 g4425.t1 CDD cd02188 gamma_tubulin 4 435 0.0
26 g4425.t1 Gene3D G3DSA:3.40.50.1440 - 1 269 3.9E-102
25 g4425.t1 Gene3D G3DSA:3.30.1330.20 - 270 381 2.0E-55
24 g4425.t1 Gene3D G3DSA:1.10.287.600 Helix hairpin bin 382 442 9.7E-24
3 g4425.t1 PANTHER PTHR11588:SF79 TUBULIN GAMMA-2 CHAIN 1 442 3.4E-258
4 g4425.t1 PANTHER PTHR11588 TUBULIN 1 442 3.4E-258
18 g4425.t1 PRINTS PR01161 Tubulin signature 11 31 3.0E-63
10 g4425.t1 PRINTS PR01164 Gamma-tubulin signature 31 51 2.9E-78
16 g4425.t1 PRINTS PR01161 Tubulin signature 52 71 3.0E-63
15 g4425.t1 PRINTS PR01161 Tubulin signature 96 107 3.0E-63
17 g4425.t1 PRINTS PR01161 Tubulin signature 108 132 3.0E-63
5 g4425.t1 PRINTS PR01164 Gamma-tubulin signature 116 131 2.9E-78
20 g4425.t1 PRINTS PR01161 Tubulin signature 134 152 3.0E-63
21 g4425.t1 PRINTS PR01161 Tubulin signature 153 174 3.0E-63
14 g4425.t1 PRINTS PR01161 Tubulin signature 179 192 3.0E-63
11 g4425.t1 PRINTS PR01164 Gamma-tubulin signature 193 206 2.9E-78
19 g4425.t1 PRINTS PR01161 Tubulin signature 193 213 3.0E-63
9 g4425.t1 PRINTS PR01164 Gamma-tubulin signature 251 262 2.9E-78
12 g4425.t1 PRINTS PR01164 Gamma-tubulin signature 286 301 2.9E-78
6 g4425.t1 PRINTS PR01164 Gamma-tubulin signature 339 362 2.9E-78
8 g4425.t1 PRINTS PR01164 Gamma-tubulin signature 364 384 2.9E-78
13 g4425.t1 PRINTS PR01161 Tubulin signature 380 408 3.0E-63
7 g4425.t1 PRINTS PR01164 Gamma-tubulin signature 420 443 2.9E-78
1 g4425.t1 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 4 214 3.7E-67
2 g4425.t1 Pfam PF03953 Tubulin C-terminal domain 264 392 1.0E-48
28 g4425.t1 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 142 148 -
29 g4425.t1 SMART SM00864 Tubulin_4 48 247 3.5E-59
30 g4425.t1 SMART SM00865 Tubulin_C_4 249 393 2.7E-27
22 g4425.t1 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 4 246 1.06E-83
23 g4425.t1 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 247 442 1.77E-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

Pathway

  • This transcript belongs to the following pathways

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