Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-5C.

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_1 g14309 g14309.t11 TTS g14309.t11 36551615 36551615
chr_1 g14309 g14309.t11 isoform g14309.t11 36551616 36555404
chr_1 g14309 g14309.t11 exon g14309.t11.exon1 36551616 36553049
chr_1 g14309 g14309.t11 cds g14309.t11.CDS1 36551932 36553014
chr_1 g14309 g14309.t11 exon g14309.t11.exon2 36555209 36555404
chr_1 g14309 g14309.t11 TSS g14309.t11 36555404 36555404

Sequences

>g14309.t11 Gene=g14309 Length=1630
ATCAATGAAAGTCTGAAAGTCTAGCTGTATAGACGAAAAAATAGTAATTTTAGTAATAAA
AAGCTAAGAAACTTGAAGTTTTTTGAAACCCCAAGGATAAATTGAATAAGCTTCAACAAA
TTTGTTAAACTCTCATAGTTTAGTGGAATAATTTATTATATTAATAAACACTTTTTAAAT
AAACCAAATGTAAGTAAAGTTGCTGCATTGGTCGTTGACAATGGATCAGGAATGTGCAAA
GCCGGTTTTGCTGGTGATGATGCACCACGTGCCGTTTTCCCATCAATTGTCGGTCGTCCA
CGTCATCAAGGCGTTATGGTCGGTATGGGACAAAAGGACTCATATGTTGGTGATGAGGCT
CAAAGCAAAAGAGGTATTCTTACCTTGAAATATCCAATTGAACACGGTATTGTTACAAAC
TGGGATGATATGGAAAAGATCTGGCATCATACTTTCTACAATGAACTCCGTGTTGCACCT
GAAGAACATCCAGTCTTGCTTACCGAAGCTCCATTAAATCCAAAAGCAAATCGTGAAAAG
ATGACACAAATTATGTTCGAGACATTCAACACACCAGCTATGTATGTTGCAATTCAAGCT
GTCCTCTCATTGTATGCCTCAGGTCGTACAACTGGTATTGTTTTGGATTCTGGTGATGGT
GTTTCACACACAGTTCCAATTTACGAAGGTTATGCTTTGCCACATGCTATCCTTCGTCTT
GATTTGGCCGGTCGTGATTTGACAGATTATTTGATGAAAATCTTAACCGAACGTGGATAC
TCATTCACAACCACTGCCGAACGTGAAATTGTTCGTGATATCAAAGAAAAATTGTGCTAT
GTTGCACTTGACTTTGAACAAGAAATGGCAACAGCTGCTTCATCAAGCTCATTGGAGAAA
TCATATGAATTGCCTGATGGACAAGTCATCACAATCGGAAATGAACGATTCCGTTGTCCA
GAAGCATTGTTCCAGCCATCATTCTTGGGTATGGAAGCATGTGGTATTCACGAGACAACA
TACAATTCAATCATGAAGTGTGACGTTGATATCCGTAAAGACTTGTATGCCAACACAGTC
TTGTCAGGTGGCACAACAATGTACCCAGGTATCGCTGATCGTATGCAAAAGGAAATTACA
GCATTAGCTCCATCAACAATGAAGATCAAAATTATTGCACCACCAGAACGTAAATACTCA
GTCTGGATCGGAGGTTCAATTTTGGCATCGCTCTCAACCTTCCAACAAATGTGGATCAGC
AAACAAGAATATGATGAATCAGGCCCATCAATTGTCCACAGAAAATGCTTCTAAATTAAT
TATAATTGTAATCAATTACCACCTTTAAGTCGTCGACATCAAGATCTTCAACCACAGAAA
CTCAAAAGACAATTGCATTTTTCACAGTTGAAATTCCATTCATTACATTCCACCACTTAC
AACATCAACTTTAAGAAAACATGTATTGTCAAAAATATTTTTTGCTCTTTTCTTTTCTAT
TATGAAAACAACATTTAAATTTAATTTAATTATTATATTACACTACTTTCTCAAAGATCA
TGAATTTATCACTCAAAAAAAAAAAATGTGCAGAAAATGAATAAAAAGAAAAAGCTTCAA
ATTTCAAATT

>g14309.t11 Gene=g14309 Length=360
MCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGI
VTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVA
IQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTE
RGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERF
RCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQK
EITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14309.t11 CDD cd00012 NBD_sugar-kinase_HSP70_actin 59 166 9.01214E-17
13 g14309.t11 Gene3D G3DSA:3.30.420.40 - 1 356 4.8E-187
14 g14309.t11 Gene3D G3DSA:3.30.420.40 - 123 323 4.8E-187
12 g14309.t11 Gene3D G3DSA:3.90.640.10 Actin; Chain A 165 257 4.8E-187
2 g14309.t11 PANTHER PTHR11937 ACTIN 1 359 6.6E-249
3 g14309.t11 PANTHER PTHR11937:SF192 ACTIN, CYTOPLASMIC 1 1 359 6.6E-249
4 g14309.t11 PRINTS PR00190 Actin signature 11 20 4.1E-58
6 g14309.t11 PRINTS PR00190 Actin signature 34 45 4.1E-58
7 g14309.t11 PRINTS PR00190 Actin signature 46 68 4.1E-58
5 g14309.t11 PRINTS PR00190 Actin signature 100 113 4.1E-58
9 g14309.t11 PRINTS PR00190 Actin signature 125 144 4.1E-58
8 g14309.t11 PRINTS PR00190 Actin signature 221 237 4.1E-58
1 g14309.t11 Pfam PF00022 Actin 1 360 4.3E-144
18 g14309.t11 ProSitePatterns PS00406 Actins signature 1. 38 48 -
17 g14309.t11 ProSitePatterns PS01132 Actins and actin-related proteins signature. 89 101 -
16 g14309.t11 ProSitePatterns PS00432 Actins signature 2. 341 349 -
19 g14309.t11 SMART SM00268 actin_3 1 360 1.1E-229
10 g14309.t11 SUPERFAMILY SSF53067 Actin-like ATPase domain 1 138 7.12E-60
11 g14309.t11 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

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