Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin, cytoplasmic A3a.

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.t9 isoform g14310.t9 36559508 36560753
chr_1 g14310 g14310.t9 exon g14310.t9.exon1 36559508 36560115
chr_1 g14310 g14310.t9 TTS g14310.t9 36559512 36559512
chr_1 g14310 g14310.t9 cds g14310.t9.CDS1 36560084 36560115
chr_1 g14310 g14310.t9 exon g14310.t9.exon2 36560220 36560753
chr_1 g14310 g14310.t9 cds g14310.t9.CDS2 36560220 36560751
chr_1 g14310 g14310.t9 TSS g14310.t9 36561081 36561081

Sequences

>g14310.t9 Gene=g14310 Length=1142
AAATGTGTGACGAAGAAGTTGCTGCATTGGTCGTTGACAATGGATCAGGAATGTGCAAAG
CCGGTTTCGCTGGTGATGATGCACCACGTGCCGTTTTCCCATCAATTGTCGGTCGTCCAC
GTCATCAAGGCGTTATGGTCGGTATGGGACAAAAGGACTCATATGTTGGTGATGAGGCTC
AAAGCAAAAGAGGTATTCTTACCTTGAAATATCCAATTGAACACGGTATTGTTACAAACT
GGGATGATATGGAAAAGATCTGGCATCATACTTTCTACAATGAACTCCGTGTTGCTCCTG
AAGAACATCCAGTCTTGCTTACCGAAGCTCCATTGAATCCAAAAGCAAATCGTGAAAAGA
TGACACAAATTATGTTCGAGACATTCAACACACCAGCTATGTATGTCTCAATTCAAGCTG
TCCTCTCATTGTATGCCTCAGGTCGTACAACTGGTATTGTTTTGGATTCTGGTGATGGCG
TTTCACACACAGTTCCAATTTACGAAGGTTATGCTTTGCCACATGCTATCCTTCATCAAA
GAAAAATTGTGCTATGTTGCACTTGACTTTGAACAAGAAATGGCAACAGCTGCTTCATCA
AGCTCATTGGAGAAATCATATGAATTGCCTGATGGACAAGTCATCACAATCGGAAATGAA
CGATTCCGTTGTCCAGAAACTCTCTTCCAACCATCATACATTGGTATGGAATCAAATGGA
ATTCACGAAACAACATACAATTCAATCATGAAGTGTGACGTTGATATCCGTAAAGACTTG
TATGCCAACACAGTCTTGTCAGGTGGCACAACAATGTTCCCAGGTATCGCTGATCGTATG
CAAAAGGAAATTACAGCATTAGCTCCATCAACAATGAAGATCAAAATTATTGCACCACCA
GAACGTAAATACTCAGTCTGGATCGGAGGTTCAATTTTGGCATCGCTCTCAACCTTCCAA
CAAATGTGGATCAGCAAACAAGAATATGATGAATCAGGCCCATCAATTGTCCACAGAAAA
TGCTTCTAAATTTTGCCAACTAAAGATTTTTATTTTAAAATTTATTTTTCTAACTAAAGA
CTGCATGTTAAAACACTCTTTCGGTCTTTAATAAAGTACTTTATTAAAATGCTGATGTAA
AA

>g14310.t9 Gene=g14310 Length=187
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVSIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILHQR
KIVLCCT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g14310.t9 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 176 1.473E-19
11 g14310.t9 Gene3D G3DSA:2.30.36.70 Actin; Chain A 35 72 2.0E-29
12 g14310.t9 Gene3D G3DSA:3.30.420.40 - 152 178 1.1E-7
2 g14310.t9 PANTHER PTHR11937:SF423 CYTOPLASMATIC ACTIN 1 179 3.6E-121
3 g14310.t9 PANTHER PTHR11937 ACTIN 1 179 3.6E-121
6 g14310.t9 PRINTS PR00190 Actin signature 27 36 8.1E-48
7 g14310.t9 PRINTS PR00190 Actin signature 50 61 8.1E-48
8 g14310.t9 PRINTS PR00190 Actin signature 62 84 8.1E-48
5 g14310.t9 PRINTS PR00190 Actin signature 116 129 8.1E-48
4 g14310.t9 PRINTS PR00190 Actin signature 141 160 8.1E-48
1 g14310.t9 Pfam PF00022 Actin 4 179 1.8E-68
15 g14310.t9 ProSitePatterns PS00406 Actins signature 1. 54 64 -
14 g14310.t9 ProSitePatterns PS01132 Actins and actin-related proteins signature. 105 117 -
16 g14310.t9 SMART SM00268 actin_3 6 187 4.8E-27
9 g14310.t9 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 154 2.19E-67
10 g14310.t9 SUPERFAMILY SSF53067 Actin-like ATPase domain 147 178 1.94E-8

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