Gene loci information

Transcript annotation

  • This transcript has been annotated as 5’-AMP-activated protein kinase subunit beta-2.

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.t2 TSS g14858.t2 2679914 2679914
chr_4 g14858 g14858.t2 isoform g14858.t2 2679995 2681958
chr_4 g14858 g14858.t2 exon g14858.t2.exon1 2679995 2680027
chr_4 g14858 g14858.t2 exon g14858.t2.exon2 2680738 2680803
chr_4 g14858 g14858.t2 exon g14858.t2.exon3 2680881 2681019
chr_4 g14858 g14858.t2 exon g14858.t2.exon4 2681074 2681336
chr_4 g14858 g14858.t2 cds g14858.t2.CDS1 2681232 2681336
chr_4 g14858 g14858.t2 exon g14858.t2.exon5 2681526 2681712
chr_4 g14858 g14858.t2 cds g14858.t2.CDS2 2681526 2681712
chr_4 g14858 g14858.t2 exon g14858.t2.exon6 2681768 2681958
chr_4 g14858 g14858.t2 cds g14858.t2.CDS3 2681768 2681958
chr_4 g14858 g14858.t2 TTS g14858.t2 2682175 2682175

Sequences

>g14858.t2 Gene=g14858 Length=879
AAGTGTTTCTTCGCATGTTGGAAACTTAATTGCGTGCAATGCCACGAGAGCGTCACAAGT
CAGGATCACAAGACCTCATACCAGGCTCACCAATGAGAACTGATGAACAAGCTTTTGTGT
TTGATAAACGTCCAATTAATAATAATCGATTGACAGTTGAAGATGATGACTCCATGTATT
CACGGTCTTTACCGCATGAGAGTGAATTAGCAAGTCGACTTCATAGACAAAGAGGTTTCA
AATACATTAAGTGAAGGAACAGGACAAAATATCACAAAATCACCAGATCAAATAATTGAA
GGTGAAAAAATTGCATTACCAACGGTCTTTAAATGGGATGGTGGTGGAAAACAAGTTTAT
ATTAGTGGAACATTTAGCAATTGGAAAGCACTGCCAATGGTTAAATCTCATGGTGATTTT
GTGACAATTATTGATTTACCTGAAGGAGAACATCAATTTAAGTTCTGTGTTGATGGCGAA
TGGAAGCATGATCCGAAAATGAAAAACATCGAAAATGACCTAGGAAGTCGAAATAATATG
CTGAGTGTTCGTCGTAGTGATTTTGAAGTTTTTCAAGCTTTAGCTAAGGATTCTGAGGAC
ACTGGAGGTTCTGAAACAAAAGAATATTCACAAGATATCCCACAAATAAAACCATGGGAA
AAAGTAAATGGGCCACCTATTTTACCACCACATTTATTGCAAGTCATATTGAATAAGGAT
ACACCATTATCAGTTGAACCAACTTTGCTACCAGAACCAAACCATGTTATGCTAAATCAT
TTGTATGCATTGAGTATTAAAGATTCAGTCATGGTCTTATCAGCATCTCATCGTTATCGC
AAAAAATATGTTACAACACTTCTTTATAAGCCAATTTAA

>g14858.t2 Gene=g14858 Length=160
MVKSHGDFVTIIDLPEGEHQFKFCVDGEWKHDPKMKNIENDLGSRNNMLSVRRSDFEVFQ
ALAKDSEDTGGSETKEYSQDIPQIKPWEKVNGPPILPPHLLQVILNKDTPLSVEPTLLPE
PNHVMLNHLYALSIKDSVMVLSASHRYRKKYVTTLLYKPI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14858.t2 CDD cd02859 E_set_AMPKbeta_like_N 1 51 5.27669E-19
9 g14858.t2 Gene3D G3DSA:2.60.40.10 Immunoglobulins 1 69 5.0E-17
10 g14858.t2 Gene3D G3DSA:3.30.160.760 - 74 160 1.3E-33
8 g14858.t2 MobiDBLite mobidb-lite consensus disorder prediction 64 83 -
3 g14858.t2 PANTHER PTHR10343:SF83 5’-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 2 160 1.9E-66
4 g14858.t2 PANTHER PTHR10343 5’-AMP-ACTIVATED PROTEIN KINASE , BETA SUBUNIT 2 160 1.9E-66
1 g14858.t2 Pfam PF16561 Glycogen recognition site of AMP-activated protein kinase 1 56 6.6E-18
2 g14858.t2 Pfam PF04739 5’-AMP-activated protein kinase beta subunit, interaction domain 91 159 9.2E-25
7 g14858.t2 SMART SM01010 AMPKBI_2 70 160 3.3E-47
5 g14858.t2 SUPERFAMILY SSF81296 E set domains 1 57 2.94E-12
6 g14858.t2 SUPERFAMILY SSF160219 AMPKBI-like 72 160 7.32E-33

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

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