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.t9 isoform g14309.t9 36551599 36554027
chr_1 g14309 g14309.t9 exon g14309.t9.exon1 36551599 36553016
chr_1 g14309 g14309.t9 TTS g14309.t9 36551615 36551615
chr_1 g14309 g14309.t9 cds g14309.t9.CDS1 36551932 36553014
chr_1 g14309 g14309.t9 exon g14309.t9.exon2 36553948 36554027
chr_1 g14309 g14309.t9 TSS g14309.t9 36554119 36554119

Sequences

>g14309.t9 Gene=g14309 Length=1498
GCTGTGTTTTAAAATTGCCGTAAAAGCATTCTCAAATCACCAATACTTTCTTTATTGTGA
AATTTAAGGACTAAAACAAGGAATGTGCAAAGCCGGTTTTGCTGGTGATGATGCACCACG
TGCCGTTTTCCCATCAATTGTCGGTCGTCCACGTCATCAAGGCGTTATGGTCGGTATGGG
ACAAAAGGACTCATATGTTGGTGATGAGGCTCAAAGCAAAAGAGGTATTCTTACCTTGAA
ATATCCAATTGAACACGGTATTGTTACAAACTGGGATGATATGGAAAAGATCTGGCATCA
TACTTTCTACAATGAACTCCGTGTTGCACCTGAAGAACATCCAGTCTTGCTTACCGAAGC
TCCATTAAATCCAAAAGCAAATCGTGAAAAGATGACACAAATTATGTTCGAGACATTCAA
CACACCAGCTATGTATGTTGCAATTCAAGCTGTCCTCTCATTGTATGCCTCAGGTCGTAC
AACTGGTATTGTTTTGGATTCTGGTGATGGTGTTTCACACACAGTTCCAATTTACGAAGG
TTATGCTTTGCCACATGCTATCCTTCGTCTTGATTTGGCCGGTCGTGATTTGACAGATTA
TTTGATGAAAATCTTAACCGAACGTGGATACTCATTCACAACCACTGCCGAACGTGAAAT
TGTTCGTGATATCAAAGAAAAATTGTGCTATGTTGCACTTGACTTTGAACAAGAAATGGC
AACAGCTGCTTCATCAAGCTCATTGGAGAAATCATATGAATTGCCTGATGGACAAGTCAT
CACAATCGGAAATGAACGATTCCGTTGTCCAGAAGCATTGTTCCAGCCATCATTCTTGGG
TATGGAAGCATGTGGTATTCACGAGACAACATACAATTCAATCATGAAGTGTGACGTTGA
TATCCGTAAAGACTTGTATGCCAACACAGTCTTGTCAGGTGGCACAACAATGTACCCAGG
TATCGCTGATCGTATGCAAAAGGAAATTACAGCATTAGCTCCATCAACAATGAAGATCAA
AATTATTGCACCACCAGAACGTAAATACTCAGTCTGGATCGGAGGTTCAATTTTGGCATC
GCTCTCAACCTTCCAACAAATGTGGATCAGCAAACAAGAATATGATGAATCAGGCCCATC
AATTGTCCACAGAAAATGCTTCTAAATTAATTATAATTGTAATCAATTACCACCTTTAAG
TCGTCGACATCAAGATCTTCAACCACAGAAACTCAAAAGACAATTGCATTTTTCACAGTT
GAAATTCCATTCATTACATTCCACCACTTACAACATCAACTTTAAGAAAACATGTATTGT
CAAAAATATTTTTTGCTCTTTTCTTTTCTATTATGAAAACAACATTTAAATTTAATTTAA
TTATTATATTACACTACTTTCTCAAAGATCATGAATTTATCACTCAAAAAAAAAAAATGT
GCAGAAAATGAATAAAAAGAAAAAGCTTCAAATTTCAAATTCATATAAAATTTTTCTT

>g14309.t9 Gene=g14309 Length=360
MCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGI
VTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVA
IQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTE
RGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERF
RCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQK
EITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14309.t9 CDD cd00012 NBD_sugar-kinase_HSP70_actin 59 166 9.01214E-17
13 g14309.t9 Gene3D G3DSA:3.30.420.40 - 1 356 4.8E-187
14 g14309.t9 Gene3D G3DSA:3.30.420.40 - 123 323 4.8E-187
12 g14309.t9 Gene3D G3DSA:3.90.640.10 Actin; Chain A 165 257 4.8E-187
2 g14309.t9 PANTHER PTHR11937 ACTIN 1 359 6.6E-249
3 g14309.t9 PANTHER PTHR11937:SF192 ACTIN, CYTOPLASMIC 1 1 359 6.6E-249
4 g14309.t9 PRINTS PR00190 Actin signature 11 20 4.1E-58
6 g14309.t9 PRINTS PR00190 Actin signature 34 45 4.1E-58
7 g14309.t9 PRINTS PR00190 Actin signature 46 68 4.1E-58
5 g14309.t9 PRINTS PR00190 Actin signature 100 113 4.1E-58
9 g14309.t9 PRINTS PR00190 Actin signature 125 144 4.1E-58
8 g14309.t9 PRINTS PR00190 Actin signature 221 237 4.1E-58
1 g14309.t9 Pfam PF00022 Actin 1 360 4.3E-144
18 g14309.t9 ProSitePatterns PS00406 Actins signature 1. 38 48 -
17 g14309.t9 ProSitePatterns PS01132 Actins and actin-related proteins signature. 89 101 -
16 g14309.t9 ProSitePatterns PS00432 Actins signature 2. 341 349 -
19 g14309.t9 SMART SM00268 actin_3 1 360 1.1E-229
10 g14309.t9 SUPERFAMILY SSF53067 Actin-like ATPase domain 1 138 7.12E-60
11 g14309.t9 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