Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-42A.

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 g14310 g14310.t4 isoform g14310.t4 36559506 36560552
chr_1 g14310 g14310.t4 exon g14310.t4.exon1 36559506 36559826
chr_1 g14310 g14310.t4 TTS g14310.t4 36559512 36559512
chr_1 g14310 g14310.t4 cds g14310.t4.CDS1 36559621 36559826
chr_1 g14310 g14310.t4 exon g14310.t4.exon2 36559947 36560552
chr_1 g14310 g14310.t4 cds g14310.t4.CDS2 36559947 36560505
chr_1 g14310 g14310.t4 TSS g14310.t4 36561081 36561081

Sequences

>g14310.t4 Gene=g14310 Length=927
CCTTGAAATATCCAATTGAACACGGTATTGTTACAAACTGGGATGATATGGAAAAGATCT
GGCATCATACTTTCTACAATGAACTCCGTGTTGCTCCTGAAGAACATCCAGTCTTGCTTA
CCGAAGCTCCATTGAATCCAAAAGCAAATCGTGAAAAGATGACACAAATTATGTTCGAGA
CATTCAACACACCAGCTATGTATGTCTCAATTCAAGCTGTCCTCTCATTGTATGCCTCAG
GTCGTACAACTGGTATTGTTTTGGATTCTGGTGATGGCGTTTCACACACAGTTCCAATTT
ACGAAGGTTATGCTTTGCCACATGCTATCCTTCGTCTTGATTTGGCCGGTCGTGATTTAA
CTGATTTCCTTATGAAAATCTTAACCGAACGTGGTTATACTTTCACAACCACTGCCGAAC
GTGAAATTGTCCGTGATATCAAAGAAAAATTGTGCTATGTTGCACTTGACTTTGAACAAG
AAATGGCAACAGCTGCTTCATCAAGCTCATTGGAGAAATCATATGAATTGCCTGATGGAC
AAGTCATCACAATCGGAAATGAACGATTCCGTTGTCCAGAAACTCTCTTCCAACCATCAT
ACATTGGTATCGCTGATCGTATGCAAAAGGAAATTACAGCATTAGCTCCATCAACAATGA
AGATCAAAATTATTGCACCACCAGAACGTAAATACTCAGTCTGGATCGGAGGTTCAATTT
TGGCATCGCTCTCAACCTTCCAACAAATGTGGATCAGCAAACAAGAATATGATGAATCAG
GCCCATCAATTGTCCACAGAAAATGCTTCTAAATTTTGCCAACTAAAGATTTTTATTTTA
AAATTTATTTTTCTAACTAAAGACTGCATGTTAAAACACTCTTTCGGTCTTTAATAAAGT
ACTTTATTAAAATGCTGATGTAAAATA

>g14310.t4 Gene=g14310 Length=254
MEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVSIQAVLS
LYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDFLMKILTERGYTFT
TTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPETL
FQPSYIGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQE
YDESGPSIVHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g14310.t4 CDD cd00012 NBD_sugar-kinase_HSP70_actin 1 100 4.56998E-15
16 g14310.t4 Gene3D G3DSA:3.30.420.40 - 1 55 1.3E-94
15 g14310.t4 Gene3D G3DSA:3.30.420.40 - 56 99 1.3E-94
12 g14310.t4 Gene3D G3DSA:3.90.640.10 Actin; Chain A 100 187 1.3E-94
13 g14310.t4 Gene3D G3DSA:3.30.420.40 - 188 216 2.1E-27
14 g14310.t4 Gene3D G3DSA:3.30.420.40 - 217 250 2.1E-27
2 g14310.t4 PANTHER PTHR11937 ACTIN 1 188 3.0E-160
4 g14310.t4 PANTHER PTHR11937:SF470 ACTIN-2 1 188 3.0E-160
3 g14310.t4 PANTHER PTHR11937 ACTIN 185 253 3.0E-160
5 g14310.t4 PANTHER PTHR11937:SF470 ACTIN-2 185 253 3.0E-160
8 g14310.t4 PRINTS PR00190 Actin signature 3 21 6.5E-42
9 g14310.t4 PRINTS PR00190 Actin signature 34 47 6.5E-42
7 g14310.t4 PRINTS PR00190 Actin signature 59 78 6.5E-42
6 g14310.t4 PRINTS PR00190 Actin signature 155 171 6.5E-42
1 g14310.t4 Pfam PF00022 Actin 1 187 1.8E-67
19 g14310.t4 ProSitePatterns PS01132 Actins and actin-related proteins signature. 23 35 -
18 g14310.t4 ProSitePatterns PS00432 Actins signature 2. 235 243 -
20 g14310.t4 SMART SM00268 actin_3 1 254 2.7E-111
10 g14310.t4 SUPERFAMILY SSF53067 Actin-like ATPase domain 1 72 2.72E-30
11 g14310.t4 SUPERFAMILY SSF53067 Actin-like ATPase domain 66 254 8.1E-76

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. There were no conditions that were differentially expressed