General information for g5950.t1
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.t1 | isoform | g5950.t1 | 12985405 | 12997425 |
| chr_2 | g5950 | g5950.t1 | exon | g5950.t1.exon1 | 12985405 | 12985564 |
| chr_2 | g5950 | g5950.t1 | cds | g5950.t1.CDS1 | 12985405 | 12985564 |
| chr_2 | g5950 | g5950.t1 | exon | g5950.t1.exon2 | 12995721 | 12995902 |
| chr_2 | g5950 | g5950.t1 | cds | g5950.t1.CDS2 | 12995721 | 12995902 |
| chr_2 | g5950 | g5950.t1 | exon | g5950.t1.exon3 | 12995968 | 12996814 |
| chr_2 | g5950 | g5950.t1 | cds | g5950.t1.CDS3 | 12995968 | 12996814 |
| chr_2 | g5950 | g5950.t1 | exon | g5950.t1.exon4 | 12996881 | 12997211 |
| chr_2 | g5950 | g5950.t1 | cds | g5950.t1.CDS4 | 12996881 | 12997211 |
| chr_2 | g5950 | g5950.t1 | exon | g5950.t1.exon5 | 12997281 | 12997425 |
| chr_2 | g5950 | g5950.t1 | cds | g5950.t1.CDS5 | 12997281 | 12997425 |
| chr_2 | g5950 | g5950.t1 | TTS | g5950.t1 | 12997494 | 12997494 |
| chr_2 | g5950 | g5950.t1 | TSS | g5950.t1 | NA | NA |
Sequences
>g5950.t1 Gene=g5950 Length=1665
ATGGACCAACTACAACCACAACTACTATCAGATCAGCAAAAGAAGGCAAAAAACAAACGG
AATCGTAACATTGAGAGTGCTGCTGAAATGCCAAGAGTTAGGAGAAAAACTAAAGGGCAA
TCAGACGTGGCGCCGAGAAACAGAAAGAAGAAGGCACATGGCTTAAGTTGTTATTGCGAA
GGACATTGTCCATCAAATACACAAAATGGAACATGCGAAGTTAAATTCGGCGGACAATGT
TTTTCAATGGTTGAAGAAGTCATTGATGAACAAACAGGTCTTATGGAACCAGAATATTCT
TTTGGATGCATATCAGCTGATCAAACTTCAGGTCTTTTACAGTGCAATGCAGGAAAAAGT
GCTCAAATTCATGGCACAAATATAATTTGTTGCTCTGATGGTGATTTCTGTAATCGAGAT
AAATTTCCTGATTACACACCTCGTACAACGACTTCACCTCCAATTGAACCAATACAACCC
GCCAATATGTCAAACTTGACTTACATCGTTCTATTTGCATCGATGTTAGCCTGCTTAGCT
GTCTTTATGATCATCATTCTATGTGTGTATATCTCATATAAACGACGTGAGAATAAAAGA
TTAAGAAGAAATCAAAGACTGATGGAACCAAATTGGAATGGAAGTGCAGCAAATCAAATG
TCACCATTAGCCAATCTTGTTGAGCAGAGTTCTGGTTCTGGAAGTGGTCTACCGTTACTT
GTACAAAGAACGATCGCTAAGCAAATACAAATGGTTGAATCAATAGGAAAAGGTCGATAT
GGTGAAGTTTGGTTAGCAAGATGGCGTGATGAAAAAGTTGCTGCCAAAGTATTTTTCACA
ACTGAAGAAGCTTCATGGTTTAGAGAAACTGAAATTTATCAGACAGTTCTTATGCGACAT
GAAAACATTTTGGGATTCATTGCAGCCGATATCAAAGGCACTGGCTCATGGACTCAAATG
TTATTAATTACTGATTATCATGAATTAGGAAGTCTTCATGATTATTTACAAAAACGCGTT
CTTAATCCTCAAATGGTGAAAACTTTGGCATTATCGTTAGCATCTGGCTTAGCACATTTG
CATACTGAAATTTTTGGAACACCTGGGAAGCCAGCAATCGCTCATCGTGATTTGAAATCT
AAAAATATCCTCGTTAAATATAATGGACAATGTGCAATTGCTGATTTCGGTCTTGCTGTA
AAATATACATCAGAATCAGATGAAGTTCAAATTGCACCAAATTCACGTGTTGGTACACGT
CGTTATATGGCAAATGAAGTTTTAGATCAATCAATGGACATGATGTCTTTTGAATCATTC
AAAATGGCTGATATATATTCACTTGGTCTCATATTTTGGGAAATTTGTAGAAGATGCATT
ACATCAATCTCACCATCAAAAAATACTACATGTGAAGACTATGCTCTTCCATACCATGAT
GTTGTTCCTTCAGATCCAAGCTTTCAAGATATGTACGATGCTGTTTGTGTGAAAGGCATT
CGACCACCAGTGCCGCAAAGATGGCTACAAGAAGATGTTCTTGCAATGCTCTCGAAGATC
ATGCAAGAATGTTGGCATCCAAATCCTGCTGTTCGTCTAACAGCACTTCGTGTCAAAAAG
TCACTCAACAAACTTAGTGGAGACGTTAAAATCAACTTAGTGTAA
>g5950.t1 Gene=g5950 Length=554
MDQLQPQLLSDQQKKAKNKRNRNIESAAEMPRVRRKTKGQSDVAPRNRKKKAHGLSCYCE
GHCPSNTQNGTCEVKFGGQCFSMVEEVIDEQTGLMEPEYSFGCISADQTSGLLQCNAGKS
AQIHGTNIICCSDGDFCNRDKFPDYTPRTTTSPPIEPIQPANMSNLTYIVLFASMLACLA
VFMIIILCVYISYKRRENKRLRRNQRLMEPNWNGSAANQMSPLANLVEQSSGSGSGLPLL
VQRTIAKQIQMVESIGKGRYGEVWLARWRDEKVAAKVFFTTEEASWFRETEIYQTVLMRH
ENILGFIAADIKGTGSWTQMLLITDYHELGSLHDYLQKRVLNPQMVKTLALSLASGLAHL
HTEIFGTPGKPAIAHRDLKSKNILVKYNGQCAIADFGLAVKYTSESDEVQIAPNSRVGTR
RYMANEVLDQSMDMMSFESFKMADIYSLGLIFWEICRRCITSISPSKNTTCEDYALPYHD
VVPSDPSFQDMYDAVCVKGIRPPVPQRWLQEDVLAMLSKIMQECWHPNPAVRLTALRVKK
SLNKLSGDVKINLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5950.t1 | Gene3D | G3DSA:2.10.60.10 | CD59 | 54 | 155 | 3.5E-19 |
| 9 | g5950.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 215 | 328 | 3.5E-49 |
| 10 | g5950.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 329 | 551 | 2.0E-57 |
| 20 | g5950.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 47 | - |
| 19 | g5950.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 13 | 47 | - |
| 4 | g5950.t1 | PANTHER | PTHR23255 | TRANSFORMING GROWTH FACTOR-BETA RECEPTOR TYPE I AND II | 50 | 549 | 1.2E-201 |
| 5 | g5950.t1 | PANTHER | PTHR23255:SF68 | RECEPTOR PROTEIN SERINE/THREONINE KINASE | 50 | 549 | 1.2E-201 |
| 3 | g5950.t1 | Pfam | PF01064 | Activin types I and II receptor domain | 55 | 140 | 6.0E-13 |
| 1 | g5950.t1 | Pfam | PF08515 | Transforming growth factor beta type I GS-motif | 226 | 247 | 2.9E-11 |
| 2 | g5950.t1 | Pfam | PF00069 | Protein kinase domain | 251 | 540 | 1.3E-36 |
| 12 | g5950.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 165 | - |
| 13 | g5950.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 166 | 193 | - |
| 11 | g5950.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 194 | 554 | - |
| 16 | g5950.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 255 | 276 | - |
| 15 | g5950.t1 | ProSitePatterns | PS00108 | Serine/Threonine protein kinases active-site signature. | 373 | 385 | - |
| 21 | g5950.t1 | ProSiteProfiles | PS51256 | GS domain profile. | 218 | 248 | 15.349 |
| 22 | g5950.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 249 | 545 | 36.414 |
| 17 | g5950.t1 | SMART | SM00467 | GS_4 | 221 | 249 | 2.1E-12 |
| 18 | g5950.t1 | SMART | SM00220 | serkin_6 | 249 | 546 | 2.2E-28 |
| 6 | g5950.t1 | SUPERFAMILY | SSF57302 | Snake toxin-like | 52 | 146 | 1.43E-8 |
| 7 | g5950.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 235 | 542 | 5.66E-66 |
| 14 | g5950.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5950/g5950.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5950.t1.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 transcript has been annotated with K13578 (bone morphogenetic protein receptor type-1B)
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.
