Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-1.

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.t11 isoform g14310.t11 36559508 36560759
chr_1 g14310 g14310.t11 exon g14310.t11.exon1 36559508 36560178
chr_1 g14310 g14310.t11 TTS g14310.t11 36559512 36559512
chr_1 g14310 g14310.t11 cds g14310.t11.CDS1 36560129 36560178
chr_1 g14310 g14310.t11 exon g14310.t11.exon2 36560301 36560759
chr_1 g14310 g14310.t11 cds g14310.t11.CDS2 36560301 36560751
chr_1 g14310 g14310.t11 TSS g14310.t11 36561081 36561081

Sequences

>g14310.t11 Gene=g14310 Length=1130
AAATAAAAATGTGTGACGAAGAAGTTGCTGCATTGGTCGTTGACAATGGATCAGGAATGT
GCAAAGCCGGTTTCGCTGGTGATGATGCACCACGTGCCGTTTTCCCATCAATTGTCGGTC
GTCCACGTCATCAAGGCGTTATGGTCGGTATGGGACAAAAGGACTCATATGTTGGTGATG
AGGCTCAAAGCAAAAGAGGTATTCTTACCTTGAAATATCCAATTGAACACGGTATTGTTA
CAAACTGGGATGATATGGAAAAGATCTGGCATCATACTTTCTACAATGAACTCCGTGTTG
CTCCTGAAGAACATCCAGTCTTGCTTACCGAAGCTCCATTGAATCCAAAAGCAAATCGTG
AAAAGATGACACAAATTATGTTCGAGACATTCAACACACCAGCTATGTATGTCTCAATTC
AAGCTGTCCTCTCATTGTATGCCTCAGGTCGTACAACTGAAAATCTTAACCGAACGTGGT
TATACTTTCACAACCACTGCCGAACGTGAAATTGTCCGTGATATCAAAGAAAAATTGTGC
TATGTTGCACTTGACTTTGAACAAGAAATGGCAACAGCTGCTTCATCAAGCTCATTGGAG
AAATCATATGAATTGCCTGATGGACAAGTCATCACAATCGGAAATGAACGATTCCGTTGT
CCAGAAACTCTCTTCCAACCATCATACATTGGTATGGAATCAAATGGAATTCACGAAACA
ACATACAATTCAATCATGAAGTGTGACGTTGATATCCGTAAAGACTTGTATGCCAACACA
GTCTTGTCAGGTGGCACAACAATGTTCCCAGGTATCGCTGATCGTATGCAAAAGGAAATT
ACAGCATTAGCTCCATCAACAATGAAGATCAAAATTATTGCACCACCAGAACGTAAATAC
TCAGTCTGGATCGGAGGTTCAATTTTGGCATCGCTCTCAACCTTCCAACAAATGTGGATC
AGCAAACAAGAATATGATGAATCAGGCCCATCAATTGTCCACAGAAAATGCTTCTAAATT
TTGCCAACTAAAGATTTTTATTTTAAAATTTATTTTTCTAACTAAAGACTGCATGTTAAA
ACACTCTTTCGGTCTTTAATAAAGTACTTTATTAAAATGCTGATGTAAAA

>g14310.t11 Gene=g14310 Length=166
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVSIQAVLSLYASGRTTENLNRTWLYFHNHCRT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14310.t11 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 151 3.75877E-15
10 g14310.t11 Gene3D G3DSA:2.30.36.70 Actin; Chain A 35 72 1.6E-29
2 g14310.t11 PANTHER PTHR11937:SF193 ACTIN, ALPHA SKELETAL MUSCLE 2 151 6.0E-102
3 g14310.t11 PANTHER PTHR11937 ACTIN 2 151 6.0E-102
6 g14310.t11 PRINTS PR00190 Actin signature 27 36 2.2E-36
7 g14310.t11 PRINTS PR00190 Actin signature 50 61 2.2E-36
8 g14310.t11 PRINTS PR00190 Actin signature 62 84 2.2E-36
5 g14310.t11 PRINTS PR00190 Actin signature 116 129 2.2E-36
4 g14310.t11 PRINTS PR00190 Actin signature 141 160 2.2E-36
1 g14310.t11 Pfam PF00022 Actin 4 150 1.2E-55
13 g14310.t11 ProSitePatterns PS00406 Actins signature 1. 54 64 -
12 g14310.t11 ProSitePatterns PS01132 Actins and actin-related proteins signature. 105 117 -
14 g14310.t11 SMART SM00268 actin_3 6 165 2.0E-10
9 g14310.t11 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 147 9.06E-66

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