General information for g5950.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bone morphogenetic protein receptor type-1B.
Parent gene
- The parent gene g5950 is located on chr_2: 12996311..12997425 (+ 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_2 | g5950 | g5950.t4 | isoform | g5950.t4 | 12996311 | 12997425 |
| chr_2 | g5950 | g5950.t4 | exon | g5950.t4.exon1 | 12996311 | 12996814 |
| chr_2 | g5950 | g5950.t4 | cds | g5950.t4.CDS1 | 12996376 | 12996814 |
| chr_2 | g5950 | g5950.t4 | exon | g5950.t4.exon2 | 12996881 | 12997200 |
| chr_2 | g5950 | g5950.t4 | cds | g5950.t4.CDS2 | 12996881 | 12997200 |
| chr_2 | g5950 | g5950.t4 | exon | g5950.t4.exon3 | 12997281 | 12997425 |
| chr_2 | g5950 | g5950.t4 | cds | g5950.t4.CDS3 | 12997281 | 12997397 |
| chr_2 | g5950 | g5950.t4 | TTS | g5950.t4 | 12997494 | 12997494 |
| chr_2 | g5950 | g5950.t4 | TSS | g5950.t4 | NA | NA |
Sequences
>g5950.t4 Gene=g5950 Length=969
AGAGTTCTGGTTCTGGAAGTGGTCTACCGTTACTTGTACAAAGAACGATCGCTAAGCAAA
TACAAATGGTTGAATCAATAGGAAAAGGTCGATATGGTGAAGTTTGGTTAGCAAGATGGC
GTGATGAAAAAGTTGCTGCCAAAGTATTTTTCACAACTGAAGAAGCTTCATGGTTTAGAG
AAACTGAAATTTATCAGACAGTTCTTATGCGACATGAAAACATTTTGGGATTCATTGCAG
CCGATATCAAAGGCACTGGCTCATGGACTCAAATGTTATTAATTACTGATTATCATGAAT
TAGGAAGTCTTCATGATTATTTACAAAAACGCGTTCTTAATCCTCAAATGGTGAAAACTT
TGGCATTATCGTTAGCATCTGGCTTAGCACATTTGCATACTGAAATTTTTGGAACACCTG
GGAAGCCAGCAATCGCTCATCGTGATTTGAAATCTAAAAATATCCTCGTTAAATATAATG
GACAATGTGCAATTGCTGATTTCGGTCTTGCTGTAAAATATACATCAGAATCAGATGAAG
TTCAAATTGCACCAAATTCACGTGTTGGTACACGTCGTTATATGGCAAATGAAGTTTTAG
ATCAATCAATGGACATGATGTCTTTTGAATCATTCAAAATGGCTGATATATATTCACTTG
GTCTCATATTTTGGGAAATTTGTAGAAGATGCATTACATCAATCTCACCATCAAAAAATA
CTACATGTGAAGACTATGCTCTTCCATACCATGATGTTGTTCCTTCAGATCCAAGCTTTC
AAGATATGTACGATGCTGTTTGTGTGAAAGGCATTCGACCACCAATGGCTACAAGAAGAT
GTTCTTGCAATGCTCTCGAAGATCATGCAAGAATGTTGGCATCCAAATCCTGCTGTTCGT
CTAACAGCACTTCGTGTCAAAAAGTCACTCAACAAACTTAGTGGAGACGTTAAAATCAAC
TTAGTGTAA
>g5950.t4 Gene=g5950 Length=291
MVESIGKGRYGEVWLARWRDEKVAAKVFFTTEEASWFRETEIYQTVLMRHENILGFIAAD
IKGTGSWTQMLLITDYHELGSLHDYLQKRVLNPQMVKTLALSLASGLAHLHTEIFGTPGK
PAIAHRDLKSKNILVKYNGQCAIADFGLAVKYTSESDEVQIAPNSRVGTRRYMANEVLDQ
SMDMMSFESFKMADIYSLGLIFWEICRRCITSISPSKNTTCEDYALPYHDVVPSDPSFQD
MYDAVCVKGIRPPMATRRCSCNALEDHARMLASKSCCSSNSTSCQKVTQQT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5950.t4 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 1 | 78 | 2.6E-37 |
| 9 | g5950.t4 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 79 | 289 | 2.6E-47 |
| 2 | g5950.t4 | PANTHER | PTHR23255 | TRANSFORMING GROWTH FACTOR-BETA RECEPTOR TYPE I AND II | 1 | 282 | 3.9E-140 |
| 3 | g5950.t4 | PANTHER | PTHR23255:SF68 | RECEPTOR PROTEIN SERINE/THREONINE KINASE | 1 | 282 | 3.9E-140 |
| 1 | g5950.t4 | Pfam | PF00069 | Protein kinase domain | 3 | 210 | 2.0E-35 |
| 7 | g5950.t4 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 5 | 26 | - |
| 6 | g5950.t4 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 123 | 135 | - |
| 10 | g5950.t4 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 1 | 291 | 34.351 |
| 5 | g5950.t4 | SMART | SM00220 | serkin_6 | 1 | 270 | 3.3E-22 |
| 4 | g5950.t4 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 2 | 218 | 1.89E-57 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5950/g5950.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5950.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0005524 | ATP binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | BP |
| GO:0007178 | transmembrane receptor protein serine/threonine kinase signaling pathway | BP |
| GO:0004675 | transmembrane receptor protein serine/threonine kinase activity | MF |
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.
