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.t15 isoform g14309.t15 36551667 36554119
chr_1 g14309 g14309.t15 exon g14309.t15.exon1 36551667 36552167
chr_1 g14309 g14309.t15 TTS g14309.t15 36551672 36551672
chr_1 g14309 g14309.t15 cds g14309.t15.CDS1 36551932 36552167
chr_1 g14309 g14309.t15 exon g14309.t15.exon2 36552243 36553070
chr_1 g14309 g14309.t15 cds g14309.t15.CDS2 36552243 36553062
chr_1 g14309 g14309.t15 exon g14309.t15.exon3 36553948 36554119
chr_1 g14309 g14309.t15 TSS g14309.t15 36554119 36554119

Sequences

>g14309.t15 Gene=g14309 Length=1501
ACTTTGAATTGAGTTGTTGAAGAGTTTAGACGTTTTCTGTGAACGGTCTTTTGAATCATT
TTTTCCAATAAAAAATTAATTAAATCAATAGTGCTGTGTTTTAAAATTGCCGTAAAAGCA
TTCTCAAATCACCAATACTTTCTTTATTGTGAAATTTAAGGACTAAAACAAGAAATCAAA
ATGTGTGACGAAGAAGTTGCTGCATTGGTCGTTGACAATGGATCAGGAATGTGCAAAGCC
GGTTTTGCTGGTGATGATGCACCACGTGCCGTTTTCCCATCAATTGTCGGTCGTCCACGT
CATCAAGGCGTTATGGTCGGTATGGGACAAAAGGACTCATATGTTGGTGATGAGGCTCAA
AGCAAAAGAGGTATTCTTACCTTGAAATATCCAATTGAACACGGTATTGTTACAAACTGG
GATGATATGGAAAAGATCTGGCATCATACTTTCTACAATGAACTCCGTGTTGCACCTGAA
GAACATCCAGTCTTGCTTACCGAAGCTCCATTAAATCCAAAAGCAAATCGTGAAAAGATG
ACACAAATTATGTTCGAGACATTCAACACACCAGCTATGTATGTTGCAATTCAAGCTGTC
CTCTCATTGTATGCCTCAGGTCGTACAACTGGTATTGTTTTGGATTCTGGTGATGGTGTT
TCACACACAGTTCCAATTTACGAAGGTTATGCTTTGCCACATGCTATCCTTCGTCTTGAT
TTGGCCGGTCGTGATTTGACAGATTATTTGATGAAAATCTTAACCGAACGTGGATACTCA
TTCACAACCACTGCCGAACGTGAAATTGTTCGTGATATCAAAGAAAAATTGTGCTATGTT
GCACTTGACTTTGAACAAGAAATGGCAACAGCTGCTTCATCAAGCTCATTGGAGAAATCA
TATGAATTGCCTGATGGACAAGTCATCACAATCGGAAATGAACGATTCCGTTGTCCAGAA
GCATTGTTCCAGCCATCATTCTTGGGTATGGAAGCATGTGTCTTGTCAGGTGGCACAACA
ATGTACCCAGGTATCGCTGATCGTATGCAAAAGGAAATTACAGCATTAGCTCCATCAACA
ATGAAGATCAAAATTATTGCACCACCAGAACGTAAATACTCAGTCTGGATCGGAGGTTCA
ATTTTGGCATCGCTCTCAACCTTCCAACAAATGTGGATCAGCAAACAAGAATATGATGAA
TCAGGCCCATCAATTGTCCACAGAAAATGCTTCTAAATTAATTATAATTGTAATCAATTA
CCACCTTTAAGTCGTCGACATCAAGATCTTCAACCACAGAAACTCAAAAGACAATTGCAT
TTTTCACAGTTGAAATTCCATTCATTACATTCCACCACTTACAACATCAACTTTAAGAAA
ACATGTATTGTCAAAAATATTTTTTGCTCTTTTCTTTTCTATTATGAAAACAACATTTAA
ATTTAATTTAATTATTATATTACACTACTTTCTCAAAGATCATGAATTTATCACTCAAAA
A

>g14309.t15 Gene=g14309 Length=351
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLD
LAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKS
YELPDGQVITIGNERFRCPEALFQPSFLGMEACVLSGGTTMYPGIADRMQKEITALAPST
MKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g14309.t15 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 182 3.99634E-20
18 g14309.t15 Gene3D G3DSA:3.30.420.40 - 3 176 3.2E-78
15 g14309.t15 Gene3D G3DSA:3.90.640.10 Actin; Chain A 181 271 1.8E-48
17 g14309.t15 Gene3D G3DSA:3.30.420.40 - 272 311 6.2E-17
16 g14309.t15 Gene3D G3DSA:3.30.420.40 - 312 349 4.8E-12
3 g14309.t15 PANTHER PTHR11937:SF477 ACTIN, CYTOPLASMIC 1 3 273 1.6E-231
5 g14309.t15 PANTHER PTHR11937 ACTIN 3 273 1.6E-231
4 g14309.t15 PANTHER PTHR11937:SF477 ACTIN, CYTOPLASMIC 1 273 350 1.6E-231
6 g14309.t15 PANTHER PTHR11937 ACTIN 273 350 1.6E-231
9 g14309.t15 PRINTS PR00190 Actin signature 27 36 3.4E-58
11 g14309.t15 PRINTS PR00190 Actin signature 50 61 3.4E-58
12 g14309.t15 PRINTS PR00190 Actin signature 62 84 3.4E-58
8 g14309.t15 PRINTS PR00190 Actin signature 116 129 3.4E-58
7 g14309.t15 PRINTS PR00190 Actin signature 141 160 3.4E-58
10 g14309.t15 PRINTS PR00190 Actin signature 237 253 3.4E-58
1 g14309.t15 Pfam PF00022 Actin 4 271 2.6E-100
2 g14309.t15 Pfam PF00022 Actin 272 351 5.1E-34
22 g14309.t15 ProSitePatterns PS00406 Actins signature 1. 54 64 -
21 g14309.t15 ProSitePatterns PS01132 Actins and actin-related proteins signature. 105 117 -
20 g14309.t15 ProSitePatterns PS00432 Actins signature 2. 332 340 -
23 g14309.t15 SMART SM00268 actin_3 6 351 3.1E-215
13 g14309.t15 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 154 6.98E-67
14 g14309.t15 SUPERFAMILY SSF53067 Actin-like ATPase domain 147 351 9.5E-85

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 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