Gene loci information

Transcript annotation

  • This transcript has been annotated as Phosphorylase b kinase gamma catalytic chain, liver/testis isoform.

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_3 g1841 g1841.t42 isoform g1841.t42 13258760 13260812
chr_3 g1841 g1841.t42 exon g1841.t42.exon1 13258760 13258857
chr_3 g1841 g1841.t42 cds g1841.t42.CDS1 13258760 13258857
chr_3 g1841 g1841.t42 exon g1841.t42.exon2 13258945 13259081
chr_3 g1841 g1841.t42 cds g1841.t42.CDS2 13258945 13259081
chr_3 g1841 g1841.t42 exon g1841.t42.exon3 13259167 13259257
chr_3 g1841 g1841.t42 cds g1841.t42.CDS3 13259167 13259257
chr_3 g1841 g1841.t42 exon g1841.t42.exon4 13259319 13259406
chr_3 g1841 g1841.t42 cds g1841.t42.CDS4 13259319 13259406
chr_3 g1841 g1841.t42 exon g1841.t42.exon5 13259461 13259657
chr_3 g1841 g1841.t42 cds g1841.t42.CDS5 13259461 13259657
chr_3 g1841 g1841.t42 exon g1841.t42.exon6 13259736 13260812
chr_3 g1841 g1841.t42 cds g1841.t42.CDS6 13259736 13259799
chr_3 g1841 g1841.t42 TSS g1841.t42 13261336 13261336
chr_3 g1841 g1841.t42 TTS g1841.t42 NA NA

Sequences

>g1841.t42 Gene=g1841 Length=1688
ATGGCAAAAGATGAGCCAGATGATGATACACTTCCTGACAAAGACGCAGCGAAAGGTTTC
TACGCAAAATATGAACCAAAAGAGGTTCTTGGACGGTGAGTTTATTTATAGAATTTACAC
ATGTACGAGTTCATTTTCCGACAAAAGCAACGAATTGACCTTGAGTCAGATTCGCTTTCG
CACTCTGCTTCTTGTTTTTTTTACTTATCACTTTGCATATTAACACATGACAAGAGTCAC
ACTCAAAAAAATCATGTGCCGCAATGATGACGAAATAAAACGAGCCCCAAAAATTTCAAC
CAATTGCTATGAGAAAGAAAAAAAAATATTCCATTCAACTTCTTCTTCGTGCCGAAAAAC
TTGTTTCAATTTATCGGGTCTATTTATATTTAGCGCTTTATAAGCAAATAAAAAATTTCC
AATTTTCAGCGTTCTTTTTCTTTTCGTAGAATCAACGAAAGTGCAATAAATTCAAATAAC
AATGAATTGTGTCAGTTCTTATACATATTCATATTATTGCTGAGATCATGTGAAAATTGA
TACAATAATAATACTTGTAGTGCATTAGCTTTATTTAAATTTTGCACACCGGTCGAAAAG
ATTTACAAAGCTCATTAGACATTTGATATTTTTATTATGGAGCTTATAAAAGATATTTAT
TTATTCTAGAAACAAACTGTAATAATAGTAAAAAAATTCCTCTAATCATGCTTTCTCTCA
TTCATATTTCAATGTCATGATCACCATGAATAATAAAAAATGAAAAATTCTATATTTGCG
CGAAAAATATTTAAAGCTACCCAGGCTTGTCTAGTTCTCGATAATTCATTCGATTATTGT
TTGAAAATAGCTACAAAACAGGTGTGTGAAAGTAAATTATTTCTTATCAATACTTTTTTA
TTTTTAGTGGCATTTCATCGGTCGTACGTCGATGTATTGATAAGGAAACTGGTAAAGAGT
ATGCGGCAAAGATTATTGATTTGGGAGCATCGGACGTAAATGATTCACATCAGATGCTCG
AAGCGACTCGTCAAGAAATTAATATTTTGAGGCAAGTTATGGGTCATCCTTATATAATTG
AATTGCAAGATGTATTCGAATCTGATGCCTTTATTTTCCTTGTTTTTGAGCTATGTCGTC
ATGGTGAATTGTTTGATTATCTTACATCTGTAGTTACATTATCTGAGAAAAAGACACGTT
ATATTATGAGACAAATTTTTGAAGGTGTTGATTATATTCATTCACGCAATATCGTCCATC
GTGACCTGAAACCCGAAAATATACTCCTCGATGACAATCTTAATGTCAAAATCACAGACT
TTGGGTTTGCTCGTCACTTAACCGATGGCATGAAACTTTATGACTTATGTGGCACACCTG
GGTATCTTGCACCCGAAACTCTTAAATGTAACATGTTCGAAGACGCACCAGGCTATTCAA
AAGAAGTCGATATGTGGGCATGTGGTGTTATTATGTTCACACTTCTTGTCGGTTGCCCTC
CATTCTGGCATCGAAAGCAGATGATAATGCTGCGAAATATCATGGAAGGAAAGTACAGTT
TTATGTCACCCGAGTGGTCAGATATTTCAGAGGATCCAAAAGATCTGATAAGAAAATGTC
TTGTGGTTGATCCCGAGAAGCGTATAACTGTTCGCGAAGCTTTGAAGCATCCATTCTTTA
ACACTGTA

>g1841.t42 Gene=g1841 Length=225
MLEATRQEINILRQVMGHPYIIELQDVFESDAFIFLVFELCRHGELFDYLTSVVTLSEKK
TRYIMRQIFEGVDYIHSRNIVHRDLKPENILLDDNLNVKITDFGFARHLTDGMKLYDLCG
TPGYLAPETLKCNMFEDAPGYSKEVDMWACGVIMFTLLVGCPPFWHRKQMIMLRNIMEGK
YSFMSPEWSDISEDPKDLIRKCLVVDPEKRITVREALKHPFFNTV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g1841.t42 Coils Coil Coil 224 225 -
7 g1841.t42 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 1 45 1.4E-13
8 g1841.t42 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 46 225 1.4E-75
2 g1841.t42 PANTHER PTHR44167 OVARIAN-SPECIFIC SERINE/THREONINE-PROTEIN KINASE LOK-RELATED 1 224 4.2E-142
3 g1841.t42 PANTHER PTHR44167:SF7 PHOSPHORYLASE KINASE CATALYTIC SUBUNIT GAMMA 1 1 224 4.2E-142
13 g1841.t42 PIRSF PIRSF000654 ILK 1 219 7.7E-27
5 g1841.t42 PRINTS PR01049 Phosphorylase kinase family signature 51 72 1.1E-8
4 g1841.t42 PRINTS PR01049 Phosphorylase kinase family signature 214 225 1.1E-8
1 g1841.t42 Pfam PF00069 Protein kinase domain 4 222 2.0E-70
11 g1841.t42 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 144 -
12 g1841.t42 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 145 165 -
10 g1841.t42 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 166 225 -
15 g1841.t42 ProSitePatterns PS00108 Serine/Threonine protein kinases active-site signature. 80 92 -
16 g1841.t42 ProSiteProfiles PS50011 Protein kinase domain profile. 1 222 48.725
14 g1841.t42 SMART SM00220 serkin_6 3 222 6.5E-81
6 g1841.t42 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 3 224 1.89E-79

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:0005978 glycogen biosynthetic process BP
GO:0005524 ATP binding MF
GO:0004689 phosphorylase kinase activity MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation BP
GO:0005516 calmodulin binding MF
GO:0005964 phosphorylase kinase complex CC

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