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.t14 isoform g14309.t14 36551667 36554095
chr_1 g14309 g14309.t14 exon g14309.t14.exon1 36551667 36552419
chr_1 g14309 g14309.t14 TTS g14309.t14 36551672 36551672
chr_1 g14309 g14309.t14 cds g14309.t14.CDS1 36551932 36552419
chr_1 g14309 g14309.t14 exon g14309.t14.exon2 36552474 36553070
chr_1 g14309 g14309.t14 cds g14309.t14.CDS2 36552474 36553062
chr_1 g14309 g14309.t14 exon g14309.t14.exon3 36553948 36554095
chr_1 g14309 g14309.t14 TSS g14309.t14 36554119 36554119

Sequences

>g14309.t14 Gene=g14309 Length=1498
TTTAGACGTTTTCTGTGAACGGTCTTTTGAATCATTTTTTCCAATAAAAAATTAATTAAA
TCAATAGTGCTGTGTTTTAAAATTGCCGTAAAAGCATTCTCAAATCACCAATACTTTCTT
TATTGTGAAATTTAAGGACTAAAACAAGAAATCAAAATGTGTGACGAAGAAGTTGCTGCA
TTGGTCGTTGACAATGGATCAGGAATGTGCAAAGCCGGTTTTGCTGGTGATGATGCACCA
CGTGCCGTTTTCCCATCAATTGTCGGTCGTCCACGTCATCAAGGCGTTATGGTCGGTATG
GGACAAAAGGACTCATATGTTGGTGATGAGGCTCAAAGCAAAAGAGGTATTCTTACCTTG
AAATATCCAATTGAACACGGTATTGTTACAAACTGGGATGATATGGAAAAGATCTGGCAT
CATACTTTCTACAATGAACTCCGTGTTGCACCTGAAGAACATCCAGTCTTGCTTACCGAA
GCTCCATTAAATCCAAAAGCAAATCGTGAAAAGATGACACAAATTATGTTCGAGACATTC
AACACACCAGCTATGTATGTTGCAATTCAAGCTGTCCTCTCATTGTATGCCTCAGGTCGT
ACAACTGGTATTGTTTTGGATTCTGGTGATGGTGTTTCACACACAGTTCCAATTTACGAA
GGTTATGCTTTGCCACATGCTATCCTTCGTCTTGATTTGGCCGGTCGTGATTTGACAGAT
TATTTGATGAAAATCTTAACCGAACAAAAATTGTGCTATGTTGCACTTGACTTTGAACAA
GAAATGGCAACAGCTGCTTCATCAAGCTCATTGGAGAAATCATATGAATTGCCTGATGGA
CAAGTCATCACAATCGGAAATGAACGATTCCGTTGTCCAGAAGCATTGTTCCAGCCATCA
TTCTTGGGTATGGAAGCATGTGGTATTCACGAGACAACATACAATTCAATCATGAAGTGT
GACGTTGATATCCGTAAAGACTTGTATGCCAACACAGTCTTGTCAGGTGGCACAACAATG
TACCCAGGTATCGCTGATCGTATGCAAAAGGAAATTACAGCATTAGCTCCATCAACAATG
AAGATCAAAATTATTGCACCACCAGAACGTAAATACTCAGTCTGGATCGGAGGTTCAATT
TTGGCATCGCTCTCAACCTTCCAACAAATGTGGATCAGCAAACAAGAATATGATGAATCA
GGCCCATCAATTGTCCACAGAAAATGCTTCTAAATTAATTATAATTGTAATCAATTACCA
CCTTTAAGTCGTCGACATCAAGATCTTCAACCACAGAAACTCAAAAGACAATTGCATTTT
TCACAGTTGAAATTCCATTCATTACATTCCACCACTTACAACATCAACTTTAAGAAAACA
TGTATTGTCAAAAATATTTTTTGCTCTTTTCTTTTCTATTATGAAAACAACATTTAAATT
TAATTTAATTATTATATTACACTACTTTCTCAAAGATCATGAATTTATCACTCAAAAA

>g14309.t14 Gene=g14309 Length=358
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLD
LAGRDLTDYLMKILTEQKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRC
PEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEI
TALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g14309.t14 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 182 2.4631E-20
15 g14309.t14 Gene3D G3DSA:3.30.420.40 - 9 354 3.9E-175
14 g14309.t14 Gene3D G3DSA:3.30.420.40 - 139 321 3.9E-175
13 g14309.t14 Gene3D G3DSA:3.90.640.10 Actin; Chain A 181 255 3.9E-175
2 g14309.t14 PANTHER PTHR11937:SF423 CYTOPLASMATIC ACTIN 1 197 2.3E-237
4 g14309.t14 PANTHER PTHR11937 ACTIN 1 197 2.3E-237
3 g14309.t14 PANTHER PTHR11937:SF423 CYTOPLASMATIC ACTIN 197 357 2.3E-237
5 g14309.t14 PANTHER PTHR11937 ACTIN 197 357 2.3E-237
8 g14309.t14 PRINTS PR00190 Actin signature 27 36 1.1E-46
9 g14309.t14 PRINTS PR00190 Actin signature 50 61 1.1E-46
10 g14309.t14 PRINTS PR00190 Actin signature 62 84 1.1E-46
7 g14309.t14 PRINTS PR00190 Actin signature 116 129 1.1E-46
6 g14309.t14 PRINTS PR00190 Actin signature 141 160 1.1E-46
1 g14309.t14 Pfam PF00022 Actin 4 197 6.5E-75
19 g14309.t14 ProSitePatterns PS00406 Actins signature 1. 54 64 -
18 g14309.t14 ProSitePatterns PS01132 Actins and actin-related proteins signature. 105 117 -
17 g14309.t14 ProSitePatterns PS00432 Actins signature 2. 339 347 -
20 g14309.t14 SMART SM00268 actin_3 6 358 4.9E-222
12 g14309.t14 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 154 7.38E-67
11 g14309.t14 SUPERFAMILY SSF53067 Actin-like ATPase domain 148 358 4.41E-90

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