Gene loci information

Transcript annotation

  • This transcript has been annotated as 5’-AMP-activated protein kinase subunit beta-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_4 g14858 g14858.t4 TSS g14858.t4 2680647 2680647
chr_4 g14858 g14858.t4 isoform g14858.t4 2680722 2681958
chr_4 g14858 g14858.t4 exon g14858.t4.exon1 2680722 2680807
chr_4 g14858 g14858.t4 exon g14858.t4.exon2 2680877 2681015
chr_4 g14858 g14858.t4 cds g14858.t4.CDS1 2680955 2681015
chr_4 g14858 g14858.t4 exon g14858.t4.exon3 2681074 2681336
chr_4 g14858 g14858.t4 cds g14858.t4.CDS2 2681074 2681336
chr_4 g14858 g14858.t4 exon g14858.t4.exon4 2681526 2681712
chr_4 g14858 g14858.t4 cds g14858.t4.CDS3 2681526 2681712
chr_4 g14858 g14858.t4 exon g14858.t4.exon5 2681768 2681958
chr_4 g14858 g14858.t4 cds g14858.t4.CDS4 2681768 2681958
chr_4 g14858 g14858.t4 TTS g14858.t4 2682175 2682175

Sequences

>g14858.t4 Gene=g14858 Length=866
ATGGGAAATCAACAAGGTGCAATGCCACGAGAGCGTCACAAGTCAGGATCACAAGACCTC
ATACCAGGCTCACCAATGAGAAGTGAGCAGCTGATGAACAAGCTTTTGTGTTTGATAAAC
GTCCAATTAATAATAATCGATTGACAGTTGAAGATGATGACTCCATGTATTCACGGTCTT
TACCGCATGAGAGTGAATTAGCAAGTCGACTTCATAGACAAAGAGCAAATACATTAAGTG
AAGGAACAGGACAAAATATCACAAAATCACCAGATCAAATAATTGAAGGTGAAAAAATTG
CATTACCAACGGTCTTTAAATGGGATGGTGGTGGAAAACAAGTTTATATTAGTGGAACAT
TTAGCAATTGGAAAGCACTGCCAATGGTTAAATCTCATGGTGATTTTGTGACAATTATTG
ATTTACCTGAAGGAGAACATCAATTTAAGTTCTGTGTTGATGGCGAATGGAAGCATGATC
CGAAAATGAAAAACATCGAAAATGACCTAGGAAGTCGAAATAATATGCTGAGTGTTCGTC
GTAGTGATTTTGAAGTTTTTCAAGCTTTAGCTAAGGATTCTGAGGACACTGGAGGTTCTG
AAACAAAAGAATATTCACAAGATATCCCACAAATAAAACCATGGGAAAAAGTAAATGGGC
CACCTATTTTACCACCACATTTATTGCAAGTCATATTGAATAAGGATACACCATTATCAG
TTGAACCAACTTTGCTACCAGAACCAAACCATGTTATGCTAAATCATTTGTATGCATTGA
GTATTAAAGATTCAGTCATGGTCTTATCAGCATCTCATCGTTATCGCAAAAAATATGTTA
CAACACTTCTTTATAAGCCAATTTAA

>g14858.t4 Gene=g14858 Length=233
MYSRSLPHESELASRLHRQRANTLSEGTGQNITKSPDQIIEGEKIALPTVFKWDGGGKQV
YISGTFSNWKALPMVKSHGDFVTIIDLPEGEHQFKFCVDGEWKHDPKMKNIENDLGSRNN
MLSVRRSDFEVFQALAKDSEDTGGSETKEYSQDIPQIKPWEKVNGPPILPPHLLQVILNK
DTPLSVEPTLLPEPNHVMLNHLYALSIKDSVMVLSASHRYRKKYVTTLLYKPI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g14858.t4 CDD cd02859 E_set_AMPKbeta_like_N 48 124 2.58924E-32
10 g14858.t4 Gene3D G3DSA:2.60.40.10 Immunoglobulins 47 142 5.4E-30
11 g14858.t4 Gene3D G3DSA:3.30.160.760 - 147 233 3.1E-33
8 g14858.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 37 -
9 g14858.t4 MobiDBLite mobidb-lite consensus disorder prediction 17 37 -
3 g14858.t4 PANTHER PTHR10343:SF83 5’-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 39 233 4.3E-80
4 g14858.t4 PANTHER PTHR10343 5’-AMP-ACTIVATED PROTEIN KINASE , BETA SUBUNIT 39 233 4.3E-80
1 g14858.t4 Pfam PF16561 Glycogen recognition site of AMP-activated protein kinase 48 129 4.6E-32
2 g14858.t4 Pfam PF04739 5’-AMP-activated protein kinase beta subunit, interaction domain 164 232 2.1E-24
7 g14858.t4 SMART SM01010 AMPKBI_2 143 233 3.3E-47
5 g14858.t4 SUPERFAMILY SSF81296 E set domains 48 130 4.2E-24
6 g14858.t4 SUPERFAMILY SSF160219 AMPKBI-like 145 233 2.22E-32

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF
GO:0050790 regulation of catalytic activity BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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