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.t7 TSS g14858.t7 2680647 2680647
chr_4 g14858 g14858.t7 isoform g14858.t7 2680722 2681958
chr_4 g14858 g14858.t7 exon g14858.t7.exon1 2680722 2681336
chr_4 g14858 g14858.t7 cds g14858.t7.CDS1 2681232 2681336
chr_4 g14858 g14858.t7 exon g14858.t7.exon2 2681526 2681712
chr_4 g14858 g14858.t7 cds g14858.t7.CDS2 2681526 2681712
chr_4 g14858 g14858.t7 exon g14858.t7.exon3 2681768 2681958
chr_4 g14858 g14858.t7 cds g14858.t7.CDS3 2681768 2681958
chr_4 g14858 g14858.t7 TTS g14858.t7 2682175 2682175

Sequences

>g14858.t7 Gene=g14858 Length=993
ATGGGAAATCAACAAGGTGCAATGCCACGAGAGCGTCACAAGTCAGGATCACAAGACCTC
ATACCAGGCTCACCAATGAGAAGTGAGTAAAAAAAATTTTTTCTCCTTGAGCAACGCAAT
TGAATTAATTAAAAAAATTCTTTCTATTTAAAAACGCAGCTGATGAACAAGCTTTTGTGT
TTGATAAACGTCCAATTAATAATAATCGATTGACAGTTGAAGATGATGACTCCATGTATT
CACGGTCTTTACCGCATGAGAGTGAATTAGCAAGTCGACTTCATAGACAAAGAGGTTTGT
AGTACAAAGTCTCAAAATATCCCAGTTGACCTCACTAAAAAAATTTTTTTAGCAAATACA
TTAAGTGAAGGAACAGGACAAAATATCACAAAATCACCAGATCAAATAATTGAAGGTGAA
AAAATTGCATTACCAACGGTCTTTAAATGGGATGGTGGTGGAAAACAAGTTTATATTAGT
GGAACATTTAGCAATTGGAAAGCACTGCCAATGGTTAAATCTCATGGTGATTTTGTGACA
ATTATTGATTTACCTGAAGGAGAACATCAATTTAAGTTCTGTGTTGATGGCGAATGGAAG
CATGATCCGAAAATGAAAAACATCGAAAATGACCTAGGAAGTCGAAATAATATGCTGAGT
GTTCGTCGTAGTGATTTTGAAGTTTTTCAAGCTTTAGCTAAGGATTCTGAGGACACTGGA
GGTTCTGAAACAAAAGAATATTCACAAGATATCCCACAAATAAAACCATGGGAAAAAGTA
AATGGGCCACCTATTTTACCACCACATTTATTGCAAGTCATATTGAATAAGGATACACCA
TTATCAGTTGAACCAACTTTGCTACCAGAACCAAACCATGTTATGCTAAATCATTTGTAT
GCATTGAGTATTAAAGATTCAGTCATGGTCTTATCAGCATCTCATCGTTATCGCAAAAAA
TATGTTACAACACTTCTTTATAAGCCAATTTAA

>g14858.t7 Gene=g14858 Length=160
MVKSHGDFVTIIDLPEGEHQFKFCVDGEWKHDPKMKNIENDLGSRNNMLSVRRSDFEVFQ
ALAKDSEDTGGSETKEYSQDIPQIKPWEKVNGPPILPPHLLQVILNKDTPLSVEPTLLPE
PNHVMLNHLYALSIKDSVMVLSASHRYRKKYVTTLLYKPI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14858.t7 CDD cd02859 E_set_AMPKbeta_like_N 1 51 5.27669E-19
9 g14858.t7 Gene3D G3DSA:2.60.40.10 Immunoglobulins 1 69 5.0E-17
10 g14858.t7 Gene3D G3DSA:3.30.160.760 - 74 160 1.3E-33
8 g14858.t7 MobiDBLite mobidb-lite consensus disorder prediction 64 83 -
3 g14858.t7 PANTHER PTHR10343:SF83 5’-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 2 160 1.9E-66
4 g14858.t7 PANTHER PTHR10343 5’-AMP-ACTIVATED PROTEIN KINASE , BETA SUBUNIT 2 160 1.9E-66
1 g14858.t7 Pfam PF16561 Glycogen recognition site of AMP-activated protein kinase 1 56 6.6E-18
2 g14858.t7 Pfam PF04739 5’-AMP-activated protein kinase beta subunit, interaction domain 91 159 9.2E-25
7 g14858.t7 SMART SM01010 AMPKBI_2 70 160 3.3E-47
5 g14858.t7 SUPERFAMILY SSF81296 E set domains 1 57 2.94E-12
6 g14858.t7 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.

Raw TPM values