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.t5 TSS g4425.t5 2115819 2115819
chr_2 g4425 g4425.t5 isoform g4425.t5 2115997 2116885
chr_2 g4425 g4425.t5 exon g4425.t5.exon1 2115997 2116885
chr_2 g4425 g4425.t5 cds g4425.t5.CDS1 2116232 2116885
chr_2 g4425 g4425.t5 TTS g4425.t5 2117515 2117515

Sequences

>g4425.t5 Gene=g4425 Length=889
TTGGCTTCGAATTTTGGAAAAGATTATGTTTAGAGCATGGAATTTCTCCATCTGGTGTGC
TTGAGGATTTTGCAACTGATGGACCCGATAGAAAGGATGTCTTTTTTTATCAAGTAAATT
TAAATTATTAATTATTTTTAAAATTATATAAAAAATAACATTTTAGGCTGATGATGATCA
CTACATTCCTAGAGCTGTTTTGCTTGATTTAGAGCCTCGAGTAATTCATACAATAATGCA
ATCACAATATGCAAAATTGTACAACCCAGAAAATATTTATCTTTCAAAAGATGGTGGTGG
TGCTGGAAATAATTGGGCAAGTGGATTTAGTCAAGGAGAAAAGTTGCAAGAGGAAGTTTT
TGATATTATCGACAGAGAGGCAGATGGAAGCGATAGTTTAGAAGGCTTTGTTTTATGCCA
TTCAATTGCTGGTGGAACAGGTAGTGGAATGGGAAGTTATATAATGGAAAGATTGTCTGA
TCATTTTCCTAAGAAACTTGTGCAAACGTATAGTGTTTTTCCGAATCAAGATGAAATTAG
TGATGTTGTTGTGCAACCGTATAACTCATTGTTGACTTTGAGGCGATTAACAAGCTGTGC
AGATTGTGTTGTGGTTTTGGACAATACAGCTCTTAATCGTATTGCAACTGATAGATTGCA
TATTGAAAATCCTTCATTCACTCAAATCAATACTCTGGTTTCAACAATCATGTCAGTTAG
CACAACTACTTTACGCTACCCTTCATACATGAATAATAATCTGATTGGTTTAACAGCACC
TCTTATTCCAACGCCACAACTTCATTTTCTCATGACTGGCTATACTCCACTCACTACTGA
AACTGATATATCAAACGTTCGGAAAACTACAGTTTTAGATGTAATGAGA

>g4425.t5 Gene=g4425 Length=218
MQSQYAKLYNPENIYLSKDGGGAGNNWASGFSQGEKLQEEVFDIIDREADGSDSLEGFVL
CHSIAGGTGSGMGSYIMERLSDHFPKKLVQTYSVFPNQDEISDVVVQPYNSLLTLRRLTS
CADCVVVLDNTALNRIATDRLHIENPSFTQINTLVSTIMSVSTTTLRYPSYMNNNLIGLT
APLIPTPQLHFLMTGYTPLTTETDISNVRKTTVLDVMR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g4425.t5 CDD cd02188 gamma_tubulin 1 218 3.9165E-166
19 g4425.t5 Coils Coil Coil 216 218 -
18 g4425.t5 Gene3D G3DSA:3.40.50.1440 - 1 192 2.5E-69
17 g4425.t5 Gene3D G3DSA:3.30.1330.20 - 193 218 1.8E-5
3 g4425.t5 PANTHER PTHR11588:SF79 TUBULIN GAMMA-2 CHAIN 2 218 2.4E-128
4 g4425.t5 PANTHER PTHR11588 TUBULIN 2 218 2.4E-128
14 g4425.t5 PRINTS PR01161 Tubulin signature 19 30 1.3E-38
13 g4425.t5 PRINTS PR01161 Tubulin signature 31 55 1.3E-38
6 g4425.t5 PRINTS PR01164 Gamma-tubulin signature 39 54 1.1E-23
11 g4425.t5 PRINTS PR01161 Tubulin signature 57 75 1.3E-38
12 g4425.t5 PRINTS PR01161 Tubulin signature 76 97 1.3E-38
9 g4425.t5 PRINTS PR01161 Tubulin signature 102 115 1.3E-38
5 g4425.t5 PRINTS PR01164 Gamma-tubulin signature 116 129 1.1E-23
10 g4425.t5 PRINTS PR01161 Tubulin signature 116 136 1.3E-38
8 g4425.t5 PRINTS PR01164 Gamma-tubulin signature 174 185 1.1E-23
7 g4425.t5 PRINTS PR01164 Gamma-tubulin signature 209 218 1.1E-23
1 g4425.t5 Pfam PF00091 Tubulin/FtsZ family, GTPase domain 4 137 4.7E-42
2 g4425.t5 Pfam PF03953 Tubulin C-terminal domain 187 218 2.7E-6
21 g4425.t5 ProSitePatterns PS00227 Tubulin subunits alpha, beta, and gamma signature. 65 71 -
22 g4425.t5 SMART SM00864 Tubulin_4 1 170 3.5E-36
15 g4425.t5 SUPERFAMILY SSF52490 Tubulin nucleotide-binding domain-like 3 169 2.35E-54
16 g4425.t5 SUPERFAMILY SSF55307 Tubulin C-terminal domain-like 170 218 1.13E-10

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