General information for g14858.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 5’-AMP-activated protein kinase subunit beta-1.
Parent gene
- The parent gene g14858 is located on chr_4: 2680722..2681958 (+ strand)
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.t3 | TSS | g14858.t3 | 2679914 | 2679914 |
| chr_4 | g14858 | g14858.t3 | isoform | g14858.t3 | 2679995 | 2681958 |
| chr_4 | g14858 | g14858.t3 | exon | g14858.t3.exon1 | 2679995 | 2680027 |
| chr_4 | g14858 | g14858.t3 | exon | g14858.t3.exon2 | 2680738 | 2680803 |
| chr_4 | g14858 | g14858.t3 | cds | g14858.t3.CDS1 | 2680743 | 2680803 |
| chr_4 | g14858 | g14858.t3 | exon | g14858.t3.exon3 | 2680881 | 2681015 |
| chr_4 | g14858 | g14858.t3 | cds | g14858.t3.CDS2 | 2680881 | 2681015 |
| chr_4 | g14858 | g14858.t3 | exon | g14858.t3.exon4 | 2681074 | 2681336 |
| chr_4 | g14858 | g14858.t3 | cds | g14858.t3.CDS3 | 2681074 | 2681336 |
| chr_4 | g14858 | g14858.t3 | exon | g14858.t3.exon5 | 2681526 | 2681712 |
| chr_4 | g14858 | g14858.t3 | cds | g14858.t3.CDS4 | 2681526 | 2681712 |
| chr_4 | g14858 | g14858.t3 | exon | g14858.t3.exon6 | 2681768 | 2681958 |
| chr_4 | g14858 | g14858.t3 | cds | g14858.t3.CDS5 | 2681768 | 2681958 |
| chr_4 | g14858 | g14858.t3 | TTS | g14858.t3 | 2682175 | 2682175 |
Sequences
>g14858.t3 Gene=g14858 Length=875
AAGTGTTTCTTCGCATGTTGGAAACTTAATTGCGTGCAATGCCACGAGAGCGTCACAAGT
CAGGATCACAAGACCTCATACCAGGCTCACCAATGAGAACTGATGAACAAGCTTTTGTGT
TTGATAAACGTCCAATTAATAATAATCGATTGACAGTTGAAGATGATGACTCCATGTATT
CACGGTCTTTACCGCATGAGAGTGAATTAGCAAGTCGACTTCATAGACAAAGAGCAAATA
CATTAAGTGAAGGAACAGGACAAAATATCACAAAATCACCAGATCAAATAATTGAAGGTG
AAAAAATTGCATTACCAACGGTCTTTAAATGGGATGGTGGTGGAAAACAAGTTTATATTA
GTGGAACATTTAGCAATTGGAAAGCACTGCCAATGGTTAAATCTCATGGTGATTTTGTGA
CAATTATTGATTTACCTGAAGGAGAACATCAATTTAAGTTCTGTGTTGATGGCGAATGGA
AGCATGATCCGAAAATGAAAAACATCGAAAATGACCTAGGAAGTCGAAATAATATGCTGA
GTGTTCGTCGTAGTGATTTTGAAGTTTTTCAAGCTTTAGCTAAGGATTCTGAGGACACTG
GAGGTTCTGAAACAAAAGAATATTCACAAGATATCCCACAAATAAAACCATGGGAAAAAG
TAAATGGGCCACCTATTTTACCACCACATTTATTGCAAGTCATATTGAATAAGGATACAC
CATTATCAGTTGAACCAACTTTGCTACCAGAACCAAACCATGTTATGCTAAATCATTTGT
ATGCATTGAGTATTAAAGATTCAGTCATGGTCTTATCAGCATCTCATCGTTATCGCAAAA
AATATGTTACAACACTTCTTTATAAGCCAATTTAA
>g14858.t3 Gene=g14858 Length=278
MPRERHKSGSQDLIPGSPMRTDEQAFVFDKRPINNNRLTVEDDDSMYSRSLPHESELASR
LHRQRANTLSEGTGQNITKSPDQIIEGEKIALPTVFKWDGGGKQVYISGTFSNWKALPMV
KSHGDFVTIIDLPEGEHQFKFCVDGEWKHDPKMKNIENDLGSRNNMLSVRRSDFEVFQAL
AKDSEDTGGSETKEYSQDIPQIKPWEKVNGPPILPPHLLQVILNKDTPLSVEPTLLPEPN
HVMLNHLYALSIKDSVMVLSASHRYRKKYVTTLLYKPI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g14858.t3 | CDD | cd02859 | E_set_AMPKbeta_like_N | 93 | 169 | 5.77833E-32 |
| 12 | g14858.t3 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 92 | 187 | 7.9E-30 |
| 13 | g14858.t3 | Gene3D | G3DSA:3.30.160.760 | - | 192 | 278 | 4.5E-33 |
| 11 | g14858.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 28 | - |
| 8 | g14858.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 44 | 76 | - |
| 9 | g14858.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 44 | 61 | - |
| 10 | g14858.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 62 | 76 | - |
| 3 | g14858.t3 | PANTHER | PTHR10343:SF83 | 5’-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-2 | 83 | 278 | 7.0E-80 |
| 4 | g14858.t3 | PANTHER | PTHR10343 | 5’-AMP-ACTIVATED PROTEIN KINASE , BETA SUBUNIT | 83 | 278 | 7.0E-80 |
| 1 | g14858.t3 | Pfam | PF16561 | Glycogen recognition site of AMP-activated protein kinase | 93 | 174 | 6.6E-32 |
| 2 | g14858.t3 | Pfam | PF04739 | 5’-AMP-activated protein kinase beta subunit, interaction domain | 209 | 277 | 2.9E-24 |
| 7 | g14858.t3 | SMART | SM01010 | AMPKBI_2 | 188 | 278 | 3.3E-47 |
| 5 | g14858.t3 | SUPERFAMILY | SSF81296 | E set domains | 93 | 175 | 5.88E-24 |
| 6 | g14858.t3 | SUPERFAMILY | SSF160219 | AMPKBI-like | 190 | 278 | 3.14E-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
- This transcript has been annotated with K07199 (5’-AMP-activated protein kinase, regulatory beta subunit)
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.
