General information for g11729.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform.
Parent gene
- The parent gene g11729 is located on chr_1: 18099008..18102024 (- 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_1 | g11729 | g11729.t1 | TTS | g11729.t1 | 18098830 | 18098830 |
| chr_1 | g11729 | g11729.t1 | isoform | g11729.t1 | 18099008 | 18102024 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon1 | 18099008 | 18099151 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS1 | 18099008 | 18099151 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon2 | 18099208 | 18099403 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS2 | 18099208 | 18099403 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon3 | 18099467 | 18099557 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS3 | 18099467 | 18099557 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon4 | 18099615 | 18099916 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS4 | 18099615 | 18099916 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon5 | 18099978 | 18100208 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS5 | 18099978 | 18100208 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon6 | 18100282 | 18100358 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS6 | 18100282 | 18100358 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon7 | 18100554 | 18100811 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS7 | 18100554 | 18100811 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon8 | 18100870 | 18101066 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS8 | 18100870 | 18101066 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon9 | 18101197 | 18101713 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS9 | 18101197 | 18101713 |
| chr_1 | g11729 | g11729.t1 | exon | g11729.t1.exon10 | 18101794 | 18102024 |
| chr_1 | g11729 | g11729.t1 | cds | g11729.t1.CDS10 | 18101794 | 18102024 |
| chr_1 | g11729 | g11729.t1 | TSS | g11729.t1 | 18102849 | 18102849 |
Sequences
>g11729.t1 Gene=g11729 Length=2244
ATGAAAGTATCCTCATCTCAATTATCGTCTAATGATGAACCAATTGAGAAAAAATTAAAT
TCAAATATACCAAAATCACCGTCATTTCATAGTGGTTTAGATTTGGTAGCTGCGAATAAA
TACGTATCAAATATATCAAAATTCAATTTTACAAACGATATGAATGGGAACACGAAATCA
AATGCTGGCGATCAGCAAGCAAACCAACAAACAATTTTTTCCTTCACAAAGTTTTTTACG
CAATCGAATCCATTAAATAATTTAAATATTGCGAGCAGCATCGTCCCTCCATTGTTGCAA
CGTCAAAATTCTGCACCAACAACTCAACAAACGCAACAAAATCAGTCGAATGATTTTTTC
AAGCCCAACAATGTGAATAAGCTTTCTTCGGTAAATAATGTTATTTCGGTAACTACATCT
TCTGGACAACCTGATTTACAACGCAAGTATTCGTTACCAATGAGCACTATTTCGTCTCAA
TCAACTGCTTCAACTGTTTCATCAACAATTTCTCAATCGTCATCTTCACAACAACAAGGA
TCTTCTGTTCATTTACCTTTTAATATTGTAAGAAAACAATCAGCTCCAACGATATCATCC
ACAATTTCATTTATCCAAACACCTGTAACTATGACACAATCTCAGTTGCAAGTTGCTCAA
CATAGCAGTCCTAGTCGTGCAAGAGATCGTAATTTATTCGACAAAATTCCAACAAATTCA
GATGTCACACAATTGACATTACTTAAAGAAGCTGATGTCAATGAGCGTGAAGAATTGTTC
ATTAAAAAAATTCGTCAATGCTGTGTTCTTTTTGACTTTACGGAGCCATTGGATGATTTA
AAATGGAAAGAAGTTAAACGAAGTGCACTTCAGGAAATGGTAGAATATATCAACAATAAT
AATGGGATTCTTACTGAAGCAATCTATCCTGAAATGATACAAATGTTTGCTATTAATTTA
TTCCGAACACTTCCACCTTCAAACAATCCAAGTGGAGCTGAATTCGATCCAGAAGAAGAT
GAACCCACACTCGAGTCATCTTGGCCACATTTACAAATTGTCTATGAACTTTTCCTAAGA
TTTCTAGAGTCACCAGATTTTCAGCCAAATATCGCAAAGCGTCACATTGATAGCCAATTT
GTGTTAAGACTACTTGATTTATTTGACTCTGAAGATCCAAGAGAGCGAGATTTTCTTAAA
ACGGTATTGCATCGCATTTATGGAAAGTTTTTGGGATTAAGAGCTTTCGTACGAAAACAA
ATTAATAACGTTTTTTATAGATTCATTTATGAAACAGAGCATCATAATGGAATAGCTGAA
CTTTTAGAAATTTTAGGATCAATCATCAATGGATTTGCGTTACCGTTAAAAGAAGAACAC
AAATCATTTTTATTAAAAGCATTATTGCCACTACATAAAGTAAAAAGTTTATCTGTATAT
CATCCGCAACTCGCTTATTGTGTTGTACAGTTCCTTGAAAAAGATCCGAGCCTTACGGAA
CCTGTTATAAAAGGTTTGTTAAAATTTTGGCCGAAAACACATAGCCCAAAAGAAGTCATG
TTTCTTAATGAACTTGAAGAAATTCTTGATGTTATTGAACCCGCTGAATTTCAAAAAGTA
ATGGTGCCGCTCTTCACACAAATATCAAAATGTGTAAGCTCACCTCATTTTCAAGTAGCT
GAGCGTGCATTATATTATTGGAACAATGATTACATCATGTCACTCATAACGGAAAATTCA
ACAGTCATTCTACCAATAATGTTTCCAGCACTATATAATAACTCAAAAACACATTGGAAT
AAGACAATTCATGGTCTCATCTATAATGCAATCAAATTATTTATGGAAATGAATCATAAG
CTTTTCGATGAATGTAACAATAAATTCAAAAATGAGAGACAATTAGAAACAGAACAGTAT
GCAAAAAGGGAAGAAATATGGCGAGAAATAGAAGAACTAGCACGAAAAAATAATCCTCAA
TTTGAAAGTTTAATAAATCATATGGAATTTTTATCGATTTCAAATCAAAATAACAACAAT
GATTACACTTTGAATGAAGATGATTATTCTAGCGATAAATTTGATCATTTTTCAAAAGAC
GCTCGTAATATTCGCAACAAGGATAAACCTTTATTAAGGAGAAAATCAGACTTACCACAA
AATTCTGGAGTTGCTAAAGTTCTCACTAATTATAAACGTGCTGACGATTTTCTAAAATCA
ACACCCGACACAAATAAATGCTAA
>g11729.t1 Gene=g11729 Length=747
MKVSSSQLSSNDEPIEKKLNSNIPKSPSFHSGLDLVAANKYVSNISKFNFTNDMNGNTKS
NAGDQQANQQTIFSFTKFFTQSNPLNNLNIASSIVPPLLQRQNSAPTTQQTQQNQSNDFF
KPNNVNKLSSVNNVISVTTSSGQPDLQRKYSLPMSTISSQSTASTVSSTISQSSSSQQQG
SSVHLPFNIVRKQSAPTISSTISFIQTPVTMTQSQLQVAQHSSPSRARDRNLFDKIPTNS
DVTQLTLLKEADVNEREELFIKKIRQCCVLFDFTEPLDDLKWKEVKRSALQEMVEYINNN
NGILTEAIYPEMIQMFAINLFRTLPPSNNPSGAEFDPEEDEPTLESSWPHLQIVYELFLR
FLESPDFQPNIAKRHIDSQFVLRLLDLFDSEDPRERDFLKTVLHRIYGKFLGLRAFVRKQ
INNVFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHKSFLLKALLPLHKVKSLSVY
HPQLAYCVVQFLEKDPSLTEPVIKGLLKFWPKTHSPKEVMFLNELEEILDVIEPAEFQKV
MVPLFTQISKCVSSPHFQVAERALYYWNNDYIMSLITENSTVILPIMFPALYNNSKTHWN
KTIHGLIYNAIKLFMEMNHKLFDECNNKFKNERQLETEQYAKREEIWREIEELARKNNPQ
FESLINHMEFLSISNQNNNNDYTLNEDDYSSDKFDHFSKDARNIRNKDKPLLRRKSDLPQ
NSGVAKVLTNYKRADDFLKSTPDTNKC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11729.t1 | Gene3D | G3DSA:1.25.10.10 | - | 253 | 653 | 0 |
| 2 | g11729.t1 | PANTHER | PTHR10257:SF89 | SERINE/THREONINE-PROTEIN PHOSPHATASE 2A 56 KDA REGULATORY SUBUNIT DELTA ISOFORM | 175 | 741 | 0 |
| 3 | g11729.t1 | PANTHER | PTHR10257 | SERINE/THREONINE PROTEIN PHOSPHATASE 2A PP2A REGULATORY SUBUNIT B | 175 | 741 | 0 |
| 6 | g11729.t1 | PIRSF | PIRSF028043 | PP2A_B56 | 2 | 743 | 0 |
| 1 | g11729.t1 | Pfam | PF01603 | Protein phosphatase 2A regulatory B subunit (B56 family) | 247 | 654 | 0 |
| 4 | g11729.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 257 | 650 | 0 |
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:0007165 | signal transduction | BP |
| GO:0019888 | protein phosphatase regulator activity | MF |
| GO:0000159 | protein phosphatase type 2A complex | CC |
KEGG
Orthology
- This transcript has been annotated with K11584 (serine/threonine-protein phosphatase 2A regulatory subunit B’)
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.
