General information for g14309.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Actin-5C.
Parent gene
- The parent gene g14309 is located on chr_1: 36552428..36555404 (- 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_1 | g14309 | g14309.t17 | isoform | g14309.t17 | 36551667 | 36554119 |
| chr_1 | g14309 | g14309.t17 | exon | g14309.t17.exon1 | 36551667 | 36553060 |
| chr_1 | g14309 | g14309.t17 | TTS | g14309.t17 | 36551672 | 36551672 |
| chr_1 | g14309 | g14309.t17 | cds | g14309.t17.CDS1 | 36551932 | 36553014 |
| chr_1 | g14309 | g14309.t17 | exon | g14309.t17.exon2 | 36553948 | 36554119 |
| chr_1 | g14309 | g14309.t17 | TSS | g14309.t17 | 36554119 | 36554119 |
Sequences
>g14309.t17 Gene=g14309 Length=1566
ACTTTGAATTGAGTTGTTGAAGAGTTTAGACGTTTTCTGTGAACGGTCTTTTGAATCATT
TTTTCCAATAAAAAATTAATTAAATCAATAGTGCTGTGTTTTAAAATTGCCGTAAAAGCA
TTCTCAAATCACCAATACTTTCTTTATTGTGAAATTTAAGGACTAAAACAAGGTGTGACG
AAGAAGTTGCTGCATTGGTCGTTGACAATGGATCAGGAATGTGCAAAGCCGGTTTTGCTG
GTGATGATGCACCACGTGCCGTTTTCCCATCAATTGTCGGTCGTCCACGTCATCAAGGCG
TTATGGTCGGTATGGGACAAAAGGACTCATATGTTGGTGATGAGGCTCAAAGCAAAAGAG
GTATTCTTACCTTGAAATATCCAATTGAACACGGTATTGTTACAAACTGGGATGATATGG
AAAAGATCTGGCATCATACTTTCTACAATGAACTCCGTGTTGCACCTGAAGAACATCCAG
TCTTGCTTACCGAAGCTCCATTAAATCCAAAAGCAAATCGTGAAAAGATGACACAAATTA
TGTTCGAGACATTCAACACACCAGCTATGTATGTTGCAATTCAAGCTGTCCTCTCATTGT
ATGCCTCAGGTCGTACAACTGGTATTGTTTTGGATTCTGGTGATGGTGTTTCACACACAG
TTCCAATTTACGAAGGTTATGCTTTGCCACATGCTATCCTTCGTCTTGATTTGGCCGGTC
GTGATTTGACAGATTATTTGATGAAAATCTTAACCGAACGTGGATACTCATTCACAACCA
CTGCCGAACGTGAAATTGTTCGTGATATCAAAGAAAAATTGTGCTATGTTGCACTTGACT
TTGAACAAGAAATGGCAACAGCTGCTTCATCAAGCTCATTGGAGAAATCATATGAATTGC
CTGATGGACAAGTCATCACAATCGGAAATGAACGATTCCGTTGTCCAGAAGCATTGTTCC
AGCCATCATTCTTGGGTATGGAAGCATGTGGTATTCACGAGACAACATACAATTCAATCA
TGAAGTGTGACGTTGATATCCGTAAAGACTTGTATGCCAACACAGTCTTGTCAGGTGGCA
CAACAATGTACCCAGGTATCGCTGATCGTATGCAAAAGGAAATTACAGCATTAGCTCCAT
CAACAATGAAGATCAAAATTATTGCACCACCAGAACGTAAATACTCAGTCTGGATCGGAG
GTTCAATTTTGGCATCGCTCTCAACCTTCCAACAAATGTGGATCAGCAAACAAGAATATG
ATGAATCAGGCCCATCAATTGTCCACAGAAAATGCTTCTAAATTAATTATAATTGTAATC
AATTACCACCTTTAAGTCGTCGACATCAAGATCTTCAACCACAGAAACTCAAAAGACAAT
TGCATTTTTCACAGTTGAAATTCCATTCATTACATTCCACCACTTACAACATCAACTTTA
AGAAAACATGTATTGTCAAAAATATTTTTTGCTCTTTTCTTTTCTATTATGAAAACAACA
TTTAAATTTAATTTAATTATTATATTACACTACTTTCTCAAAGATCATGAATTTATCACT
CAAAAA
>g14309.t17 Gene=g14309 Length=360
MCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGI
VTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVA
IQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTE
RGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERF
RCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQK
EITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g14309.t17 | CDD | cd00012 | NBD_sugar-kinase_HSP70_actin | 59 | 166 | 9.01214E-17 |
| 13 | g14309.t17 | Gene3D | G3DSA:3.30.420.40 | - | 1 | 356 | 4.8E-187 |
| 14 | g14309.t17 | Gene3D | G3DSA:3.30.420.40 | - | 123 | 323 | 4.8E-187 |
| 12 | g14309.t17 | Gene3D | G3DSA:3.90.640.10 | Actin; Chain A | 165 | 257 | 4.8E-187 |
| 2 | g14309.t17 | PANTHER | PTHR11937 | ACTIN | 1 | 359 | 6.6E-249 |
| 3 | g14309.t17 | PANTHER | PTHR11937:SF192 | ACTIN, CYTOPLASMIC 1 | 1 | 359 | 6.6E-249 |
| 4 | g14309.t17 | PRINTS | PR00190 | Actin signature | 11 | 20 | 4.1E-58 |
| 6 | g14309.t17 | PRINTS | PR00190 | Actin signature | 34 | 45 | 4.1E-58 |
| 7 | g14309.t17 | PRINTS | PR00190 | Actin signature | 46 | 68 | 4.1E-58 |
| 5 | g14309.t17 | PRINTS | PR00190 | Actin signature | 100 | 113 | 4.1E-58 |
| 9 | g14309.t17 | PRINTS | PR00190 | Actin signature | 125 | 144 | 4.1E-58 |
| 8 | g14309.t17 | PRINTS | PR00190 | Actin signature | 221 | 237 | 4.1E-58 |
| 1 | g14309.t17 | Pfam | PF00022 | Actin | 1 | 360 | 4.3E-144 |
| 18 | g14309.t17 | ProSitePatterns | PS00406 | Actins signature 1. | 38 | 48 | - |
| 17 | g14309.t17 | ProSitePatterns | PS01132 | Actins and actin-related proteins signature. | 89 | 101 | - |
| 16 | g14309.t17 | ProSitePatterns | PS00432 | Actins signature 2. | 341 | 349 | - |
| 19 | g14309.t17 | SMART | SM00268 | actin_3 | 1 | 360 | 1.1E-229 |
| 10 | g14309.t17 | SUPERFAMILY | SSF53067 | Actin-like ATPase domain | 1 | 138 | 7.12E-60 |
| 11 | g14309.t17 | SUPERFAMILY | SSF53067 | Actin-like ATPase domain | 132 | 360 | 1.9E-100 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K05692 (actin beta/gamma 1)
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.
