General information for g5214.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tubulin beta chain.
Parent gene
- The parent gene g5214 is located on chr_2: 7849772..7851305 (- strand)
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 | g5214 | g5214.t1 | TTS | g5214.t1 | 7847531 | 7847531 |
| chr_2 | g5214 | g5214.t1 | isoform | g5214.t1 | 7847807 | 7851305 |
| chr_2 | g5214 | g5214.t1 | exon | g5214.t1.exon1 | 7847807 | 7848469 |
| chr_2 | g5214 | g5214.t1 | cds | g5214.t1.CDS1 | 7847807 | 7848469 |
| chr_2 | g5214 | g5214.t1 | exon | g5214.t1.exon2 | 7848535 | 7849167 |
| chr_2 | g5214 | g5214.t1 | cds | g5214.t1.CDS2 | 7848535 | 7849167 |
| chr_2 | g5214 | g5214.t1 | exon | g5214.t1.exon3 | 7851249 | 7851305 |
| chr_2 | g5214 | g5214.t1 | cds | g5214.t1.CDS3 | 7851249 | 7851305 |
| chr_2 | g5214 | g5214.t1 | TSS | g5214.t1 | 7851441 | 7851441 |
Sequences
>g5214.t1 Gene=g5214 Length=1353
ATGAGAGAAATTGTGCATTTGCAAGTTGGTCAGTGTGGCAATCAAATTGGATCGAAATTC
TGGGAAATCATCTCAGATGAGCACGGAATTGATCCAAATGGTCACTATCATGGTGACAAT
GATTTACAATTAGAACGAATTGACGTCTATTACAATGAAGTTAATGGAAATCGTTATGTT
CCACGTTCAGTCCTTGTTGATCTTGAACCAGGCACAATGGACTCTGTTCGTCAATCACCA
TACGGAAAACTCTTCCGTCCTGACAATTTTGTGTTTGGACAATCAGGTGCTGGCAACAAT
TGGGCAAAAGGTCATTATACAGAAGGAGCAGAACTCGTTGATGCTGTCTTGGATGTGATT
CGTAAAGAGTCAGAAGGTTGTGACTGCTTGCAAGGATTCCAATTGACTCATTCACTTGGT
GGTGGCACAGGTTCAGGAATGGGAACATTATTGATTGCCAAAATCAGGGAAGAATATCCA
GATCGCATCATGAACTCTTTTTCTGTTATACCATCACCGAAAGTTTCAGACACAGTCGTT
GAGCCGTATAATGCAACTTTGTCAGTTCACCAACTGGTCGAAAACACAGACGAAACATTC
TGCATTGACAATGAGGCTCTATATGACATTTGCTTCCGTACATTGAAGTTGCAGTCGCCA
ACATATGGTGATCTCAATCATTTGGTTTCGATTACCATGTCAGGTGTAACAACTTGCTTG
CGTTTTCCTGGTCAATTAAATGCTGATTTGAGAAAACTTGCTGTCAATATGGTTCCTTTC
CCGCGTCTTCACTTTTTTATGCCGGGTTTCGCGCCATTGACAGCTAAGAACAGTCAACAA
TATCGCGCACTTAGCGTTGCTGATTTGACTCAACAAATGTTTGATGCCAAAAATATGATG
ACAGCTTGTGATCCAAGACATGGTCGTTATTTGACTGTTGCTGCAATTTTCCGTGGTCAA
ATGTCAATGAAAGAAGTTGATGAACAAATGTTGGGTGTGCAGAACAAGAACAGCAGCTAT
TTTGTCGAGTGGATTCCAAACAATGTAAAAGTTGCTGTTTGTGATATTCCACCGAGAGGA
TTAAAAATGGCAGCAACATTTATTGGCAATTCTACAGCAATTCAAGAAATTTTCAAGCGA
ATTTCTGAGCAATTTACAGCAATGTTCCGTCGTAAAGCTTTCTTGCATTGGTACACAGGT
GAAGGAATGGATGAAATGGAATTCACTGAAGCTGAGAGTAACATGAATGACTTGGTATCA
GAATATCAACAATATCAAGAAGCATCAGCTGATGATGACATTGAATTTGACGAAAATGAA
GAAATTGAGCAAAATCCAAATGAAGCTTGTTAA
>g5214.t1 Gene=g5214 Length=450
MREIVHLQVGQCGNQIGSKFWEIISDEHGIDPNGHYHGDNDLQLERIDVYYNEVNGNRYV
PRSVLVDLEPGTMDSVRQSPYGKLFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVI
RKESEGCDCLQGFQLTHSLGGGTGSGMGTLLIAKIREEYPDRIMNSFSVIPSPKVSDTVV
EPYNATLSVHQLVENTDETFCIDNEALYDICFRTLKLQSPTYGDLNHLVSITMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTAKNSQQYRALSVADLTQQMFDAKNMM
TACDPRHGRYLTVAAIFRGQMSMKEVDEQMLGVQNKNSSYFVEWIPNNVKVAVCDIPPRG
LKMAATFIGNSTAIQEIFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQEASADDDIEFDENEEIEQNPNEAC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 33 | g5214.t1 | CDD | cd02187 | beta_tubulin | 2 | 426 | 0.0 |
| 32 | g5214.t1 | Coils | Coil | Coil | 408 | 428 | - |
| 31 | g5214.t1 | Gene3D | G3DSA:3.40.50.1440 | - | 1 | 263 | 4.2E-126 |
| 30 | g5214.t1 | Gene3D | G3DSA:3.30.1330.20 | - | 264 | 373 | 1.4E-55 |
| 29 | g5214.t1 | Gene3D | G3DSA:1.10.287.600 | Helix hairpin bin | 374 | 445 | 2.5E-34 |
| 38 | g5214.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 429 | 450 | - |
| 3 | g5214.t1 | PANTHER | PTHR11588:SF100 | TUBULIN BETA-2A CHAIN | 1 | 440 | 1.8E-294 |
| 4 | g5214.t1 | PANTHER | PTHR11588 | TUBULIN | 1 | 440 | 1.8E-294 |
| 19 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 10 | 30 | 1.8E-102 |
| 9 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 41 | 58 | 3.5E-115 |
| 26 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 51 | 70 | 1.8E-102 |
| 11 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 88 | 99 | 3.5E-115 |
| 22 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 93 | 104 | 1.8E-102 |
| 23 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 106 | 130 | 1.8E-102 |
| 14 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 108 | 126 | 3.5E-115 |
| 24 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 132 | 150 | 1.8E-102 |
| 25 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 151 | 172 | 1.8E-102 |
| 6 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 152 | 164 | 3.5E-115 |
| 21 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 176 | 189 | 1.8E-102 |
| 20 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 190 | 210 | 1.8E-102 |
| 17 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 212 | 224 | 3.5E-115 |
| 8 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 230 | 239 | 3.5E-115 |
| 7 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 245 | 258 | 3.5E-115 |
| 16 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 265 | 281 | 3.5E-115 |
| 10 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 311 | 329 | 3.5E-115 |
| 15 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 329 | 343 | 3.5E-115 |
| 5 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 347 | 370 | 3.5E-115 |
| 18 | g5214.t1 | PRINTS | PR01161 | Tubulin signature | 370 | 398 | 1.8E-102 |
| 13 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 377 | 388 | 3.5E-115 |
| 12 | g5214.t1 | PRINTS | PR01163 | Beta-tubulin signature | 412 | 430 | 3.5E-115 |
| 1 | g5214.t1 | Pfam | PF00091 | Tubulin/FtsZ family, GTPase domain | 3 | 211 | 1.0E-70 |
| 2 | g5214.t1 | Pfam | PF03953 | Tubulin C-terminal domain | 261 | 382 | 6.3E-43 |
| 36 | g5214.t1 | ProSitePatterns | PS00228 | Tubulin-beta mRNA autoregulation signal. | 1 | 4 | - |
| 37 | g5214.t1 | ProSitePatterns | PS00227 | Tubulin subunits alpha, beta, and gamma signature. | 140 | 146 | - |
| 34 | g5214.t1 | SMART | SM00864 | Tubulin_4 | 47 | 244 | 2.1E-66 |
| 35 | g5214.t1 | SMART | SM00865 | Tubulin_C_4 | 246 | 383 | 2.7E-49 |
| 27 | g5214.t1 | SUPERFAMILY | SSF52490 | Tubulin nucleotide-binding domain-like | 1 | 243 | 2.09E-102 |
| 28 | g5214.t1 | SUPERFAMILY | SSF55307 | Tubulin C-terminal domain-like | 244 | 428 | 2.53E-83 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5214/g5214.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5214.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005874 | microtubule | CC |
| GO:0007017 | microtubule-based process | BP |
| GO:0005525 | GTP binding | MF |
| GO:0005200 | structural constituent of cytoskeleton | MF |
| GO:0003924 | GTPase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K07375 (tubulin beta)
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.
