General information for g1841.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phosphorylase b kinase gamma catalytic chain, liver/testis isoform.
Parent gene
- The parent gene g1841 is located on chr_3: 13260701..13261369 (- 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_3 | g1841 | g1841.t2 | TTS | g1841.t2 | 13254002 | 13254002 |
| chr_3 | g1841 | g1841.t2 | isoform | g1841.t2 | 13254268 | 13260812 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon1 | 13254268 | 13254402 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS1 | 13254268 | 13254402 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon2 | 13254475 | 13254633 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS2 | 13254475 | 13254633 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon3 | 13257131 | 13257304 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS3 | 13257131 | 13257304 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon4 | 13257998 | 13258081 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS4 | 13257998 | 13258081 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon5 | 13258760 | 13258857 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS5 | 13258760 | 13258857 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon6 | 13258945 | 13259081 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS6 | 13258945 | 13259081 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon7 | 13259167 | 13259257 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS7 | 13259167 | 13259257 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon8 | 13259319 | 13259406 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS8 | 13259319 | 13259406 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon9 | 13259461 | 13259657 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS9 | 13259461 | 13259657 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon10 | 13259736 | 13259905 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS10 | 13259736 | 13259905 |
| chr_3 | g1841 | g1841.t2 | exon | g1841.t2.exon11 | 13260718 | 13260812 |
| chr_3 | g1841 | g1841.t2 | cds | g1841.t2.CDS11 | 13260718 | 13260812 |
| chr_3 | g1841 | g1841.t2 | TSS | g1841.t2 | 13261336 | 13261336 |
Sequences
>g1841.t2 Gene=g1841 Length=1428
ATGGCAAAAGATGAGCCAGATGATGATACACTTCCTGACAAAGACGCAGCGAAAGGTTTC
TACGCAAAATATGAACCAAAAGAGGTTCTTGGACGTGGCATTTCATCGGTCGTACGTCGA
TGTATTGATAAGGAAACTGGTAAAGAGTATGCGGCAAAGATTATTGATTTGGGAGCATCG
GACGTAAATGATTCACATCAGATGCTCGAAGCGACTCGTCAAGAAATTAATATTTTGAGG
CAAGTTATGGGTCATCCTTATATAATTGAATTGCAAGATGTATTCGAATCTGATGCCTTT
ATTTTCCTTGTTTTTGAGCTATGTCGTCATGGTGAATTGTTTGATTATCTTACATCTGTA
GTTACATTATCTGAGAAAAAGACACGTTATATTATGAGACAAATTTTTGAAGGTGTTGAT
TATATTCATTCACGCAATATCGTCCATCGTGACCTGAAACCCGAAAATATACTCCTCGAT
GACAATCTTAATGTCAAAATCACAGACTTTGGGTTTGCTCGTCACTTAACCGATGGCATG
AAACTTTATGACTTATGTGGCACACCTGGGTATCTTGCACCCGAAACTCTTAAATGTAAC
ATGTTCGAAGACGCACCAGGCTATTCAAAAGAAGTCGATATGTGGGCATGTGGTGTTATT
ATGTTCACACTTCTTGTCGGTTGCCCTCCATTCTGGCATCGAAAGCAGATGATAATGCTG
CGAAATATCATGGAAGGAAAGTACAGTTTTATGTCACCCGAGTGGTCAGATATTTCAGAG
GATCCAAAAGATCTGATAAGAAAATGTCTTGTGGTTGATCCCGAGAAGCGTATAACTGTT
CGCGAAGCTTTGAAGCATCCATTCTTTAACACTGTACTTTTTGATCAAGACATCGCACCA
CTAAAGCGATCTTTATCGGCGAAAACCAGAAGATATAGCCGTATCCATGATTTAGCTTTG
AATAAGAATAAGGAGATAGCAAGTAAGGCAACAACGACAACGTCTGATAATGAACAGACT
AGTATTAATTTAAGTAATGAGACTGAGAGTATTAAAAAACAGGAACCGAAGAAACAAGTC
AATATTGTTATATCATATATTGAACAGAATGACGAGCAAGGAATTGGAAAATCGATGCGT
CGTCAAAGTCAATTTAATGCTAGGAAGAAATTTCAATTTGCTATACTATGCGTACGAGCT
ATGATAAGAATACAAAGATTGCGCTACACACCTGAACCGCTCGACATCGAAGAAGCCTTA
CGCGATCCATATCGTGTCAAAGTATTGCGTAAAGTCATCGATGCATGTGCTTTCCGCGTT
TACGGCCATTGGGTCAAGAAAGGCGAGGGACAGAATCGTGCTGCTCTCTTTGAAAACCAA
CCAAAAGTTGAACTTCATAACCTTTACATTCATCAGTTGCAAAAATAA
>g1841.t2 Gene=g1841 Length=475
MAKDEPDDDTLPDKDAAKGFYAKYEPKEVLGRGISSVVRRCIDKETGKEYAAKIIDLGAS
DVNDSHQMLEATRQEINILRQVMGHPYIIELQDVFESDAFIFLVFELCRHGELFDYLTSV
VTLSEKKTRYIMRQIFEGVDYIHSRNIVHRDLKPENILLDDNLNVKITDFGFARHLTDGM
KLYDLCGTPGYLAPETLKCNMFEDAPGYSKEVDMWACGVIMFTLLVGCPPFWHRKQMIML
RNIMEGKYSFMSPEWSDISEDPKDLIRKCLVVDPEKRITVREALKHPFFNTVLFDQDIAP
LKRSLSAKTRRYSRIHDLALNKNKEIASKATTTTSDNEQTSINLSNETESIKKQEPKKQV
NIVISYIEQNDEQGIGKSMRRQSQFNARKKFQFAILCVRAMIRIQRLRYTPEPLDIEEAL
RDPYRVKVLRKVIDACAFRVYGHWVKKGEGQNRAALFENQPKVELHNLYIHQLQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g1841.t2 | CDD | cd14093 | STKc_PhKG | 20 | 289 | 0.0 |
| 12 | g1841.t2 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 7 | 107 | 6.0E-34 |
| 13 | g1841.t2 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 108 | 298 | 6.1E-75 |
| 2 | g1841.t2 | PANTHER | PTHR44167 | OVARIAN-SPECIFIC SERINE/THREONINE-PROTEIN KINASE LOK-RELATED | 1 | 472 | 2.3E-220 |
| 3 | g1841.t2 | PANTHER | PTHR44167:SF7 | PHOSPHORYLASE KINASE CATALYTIC SUBUNIT GAMMA 1 | 1 | 472 | 2.3E-220 |
| 5 | g1841.t2 | PRINTS | PR01049 | Phosphorylase kinase family signature | 118 | 139 | 1.9E-37 |
| 10 | g1841.t2 | PRINTS | PR01049 | Phosphorylase kinase family signature | 281 | 292 | 1.9E-37 |
| 9 | g1841.t2 | PRINTS | PR01049 | Phosphorylase kinase family signature | 383 | 398 | 1.9E-37 |
| 7 | g1841.t2 | PRINTS | PR01049 | Phosphorylase kinase family signature | 399 | 417 | 1.9E-37 |
| 6 | g1841.t2 | PRINTS | PR01049 | Phosphorylase kinase family signature | 418 | 432 | 1.9E-37 |
| 8 | g1841.t2 | PRINTS | PR01049 | Phosphorylase kinase family signature | 433 | 448 | 1.9E-37 |
| 4 | g1841.t2 | PRINTS | PR01049 | Phosphorylase kinase family signature | 449 | 462 | 1.9E-37 |
| 1 | g1841.t2 | Pfam | PF00069 | Protein kinase domain | 24 | 289 | 3.1E-79 |
| 15 | g1841.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 211 | - |
| 16 | g1841.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 232 | - |
| 14 | g1841.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 233 | 475 | - |
| 20 | g1841.t2 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 30 | 53 | - |
| 19 | g1841.t2 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 147 | 159 | - |
| 21 | g1841.t2 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 24 | 289 | 53.474 |
| 18 | g1841.t2 | SMART | SM00220 | serkin_6 | 24 | 289 | 4.3E-113 |
| 11 | g1841.t2 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 20 | 302 | 8.9E-92 |
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 transcript has been annotated with K02831 (ser/thr/tyr protein kinase RAD53 [EC:2.7.11.-])
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. There were no conditions that were differentially expressed