Gene loci information

Transcript annotation

  • This transcript has been annotated as 5’-AMP-activated protein kinase catalytic subunit alpha-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_1 g12671 g12671.t1 TSS g12671.t1 25150200 25150200
chr_1 g12671 g12671.t1 isoform g12671.t1 25150483 25152395
chr_1 g12671 g12671.t1 exon g12671.t1.exon1 25150483 25150549
chr_1 g12671 g12671.t1 cds g12671.t1.CDS1 25150483 25150549
chr_1 g12671 g12671.t1 exon g12671.t1.exon2 25150625 25151046
chr_1 g12671 g12671.t1 cds g12671.t1.CDS2 25150625 25151046
chr_1 g12671 g12671.t1 exon g12671.t1.exon3 25151110 25151126
chr_1 g12671 g12671.t1 cds g12671.t1.CDS3 25151110 25151126
chr_1 g12671 g12671.t1 exon g12671.t1.exon4 25151218 25151370
chr_1 g12671 g12671.t1 cds g12671.t1.CDS4 25151218 25151370
chr_1 g12671 g12671.t1 exon g12671.t1.exon5 25151438 25152395
chr_1 g12671 g12671.t1 cds g12671.t1.CDS5 25151438 25152395
chr_1 g12671 g12671.t1 TTS g12671.t1 25152698 25152698

Sequences

>g12671.t1 Gene=g12671 Length=1617
ATGTCTGAGAGTTCAGCAGCACCTTTGATCAAGATCGGTCACTACACGCTAGGACGGACG
CTCGGAAATGGCACTTTCGGAAAAGTCAAAATTGGCGAGCATGTCGTCACAAAGCATAAA
GTGGCAATCAAAATTTTAAATCGTCAGAAAATCAAATCACTCGATGTGGTTGGAAAAATT
CGACGAGAAATTCAAAATTTAAAACTTTTTCGTCATCCTCACATAATAAAACTTTATCAA
GTGATTTCAACACCTACCGATATTTTTATGATTATGGAATATGTCAGTGGCGGTGAATTA
TTTGATTATATTGTCAAACAAGGAAAACTTCAAGAATCAGAAGCAAGAAAATTTTTCCAA
CAAATTATATCTGGTGTTGATTATTGTCATCGGCACATGATTGTTCATCGAGATTTGAAA
CCTGAAAATTTATTATTAGACCATAACATGCACGTGAAAATTGCCGATTTTGGATTGAGT
AATATGATGCTTGATGGTGAATTTTTACGAACATCATGTGGAAGTCCGAACTATGCGGCA
CCAGAAGTTATTAGTGGCAAACTCTATGCTGGTCCAGAAGTTGATATTTGGTCATGTGGA
GTCATTCTTTATGCTTTACTTTGTGGAACACTTCCATTCGATGATGAACACGTGCCTACT
TTATTTCGTAAAATCAAATCAGGAATTTTTGCCATACCTGAATATTTGAATAAGCAAGTT
GTTTCACTTTTATGTCAAATGCTTCAAGTTGATCCACTTAAAAGAGCAACAGTTGAAGAA
ATTAAGAAACATGAATGGTTCCAAAAAGATTTACCAGCCTATCTCTTCCCATCGCCAGTC
GAACAAGATTCATCAGTTATTGATATTGGCGCTGTTTCAGAAGTTTGTGAGAAATTTGGT
GTAAAAGAAGTTGAAGTTCATAATGCACTTCTTTCTGGTGATCCACATGATCAACTTGCC
ATTGCTTATCATTTAATTATTGATAATCGTCGTATGGATGAAGCTGCAAAGGCTGAAATT
AAAGATTTTTATGTTGCTTCATCACCACCACCGCAAGTCATAGTGCAAGCAACACATCCA
GTCTCTGACAATAATCCTACAAAGCCACATCCCGAACGAATTGCACCATTACGAGAGAAA
GCAGTAACATCGCATGCATTGAGCTACACTGAAGGCACAACTGTACCAGCTGATCGATTG
ATTACTCAAGATAAATATCGAGGAACACCAGTAAAAAGAGCAAAATGGCATTTGGGAATT
CGTTCACAAAGCAAACCTAATGATATTATGTTGGAAGTTTATCGTGCAATGAAAGCTTTA
GATTATGAATGGAAAGTCATCAATCCATATCATGTTCGTGTTCGTAAGAAGAATAAAGAT
GGTCGTTATGTAAAAATGTCACTGCAGCTTTATCAAGTCGATCCAAAGTCATATCTTGTC
GATTTTAAAAGTCTTACAAATGAAGAAGTTGAACAGAGTGATGATATGATAAGTTTAACG
CCACCAGTTGCAAGTCAACAACAAATTCCATTACAACAAACACCACAAATTTCTGGTCAT
CATACGATGGAATTCTTTGAAATGTGCGCATCTTTGATCATTCAATTGGCTCGTTAA

>g12671.t1 Gene=g12671 Length=538
MSESSAAPLIKIGHYTLGRTLGNGTFGKVKIGEHVVTKHKVAIKILNRQKIKSLDVVGKI
RREIQNLKLFRHPHIIKLYQVISTPTDIFMIMEYVSGGELFDYIVKQGKLQESEARKFFQ
QIISGVDYCHRHMIVHRDLKPENLLLDHNMHVKIADFGLSNMMLDGEFLRTSCGSPNYAA
PEVISGKLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFRKIKSGIFAIPEYLNKQV
VSLLCQMLQVDPLKRATVEEIKKHEWFQKDLPAYLFPSPVEQDSSVIDIGAVSEVCEKFG
VKEVEVHNALLSGDPHDQLAIAYHLIIDNRRMDEAAKAEIKDFYVASSPPPQVIVQATHP
VSDNNPTKPHPERIAPLREKAVTSHALSYTEGTTVPADRLITQDKYRGTPVKRAKWHLGI
RSQSKPNDIMLEVYRAMKALDYEWKVINPYHVRVRKKNKDGRYVKMSLQLYQVDPKSYLV
DFKSLTNEEVEQSDDMISLTPPVASQQQIPLQQTPQISGHHTMEFFEMCASLIIQLAR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g12671.t1 CDD cd14079 STKc_AMPK_alpha 12 267 0.0
13 g12671.t1 CDD cd14336 UBA_AID_AMPKalpha 284 347 9.70173E-34
12 g12671.t1 CDD cd12122 AMPKA_C 413 536 1.5762E-52
8 g12671.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 5 94 6.5E-33
9 g12671.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 95 273 5.2E-67
7 g12671.t1 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 278 338 1.5E-29
10 g12671.t1 Gene3D G3DSA:3.30.310.80 Kinase associated domain 1 419 538 1.0E-47
3 g12671.t1 PANTHER PTHR24343:SF303 5’-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2 8 493 6.1E-202
4 g12671.t1 PANTHER PTHR24343 SERINE/THREONINE KINASE 8 493 6.1E-202
2 g12671.t1 Pfam PF00069 Protein kinase domain 15 267 8.7E-77
1 g12671.t1 Pfam PF16579 Adenylate sensor of SNF1-like protein kinase 415 496 1.5E-16
15 g12671.t1 ProSitePatterns PS00107 Protein kinases ATP-binding region signature. 21 44 -
14 g12671.t1 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 134 146 -
17 g12671.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 15 267 53.064
16 g12671.t1 SMART SM00220 serkin_6 15 267 7.9E-108
6 g12671.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 12 268 2.29E-97
5 g12671.t1 SUPERFAMILY SSF103243 KA1-like 323 537 3.01E-48

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:0005524 ATP binding MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation 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.

Raw TPM values