General information for g5442.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein decapentaplegic.
Parent gene
- The parent gene g5442 is located on chr_2: 9599032..9601666 (- 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 | g5442 | g5442.t1 | TTS | g5442.t1 | 9598349 | 9598349 |
| chr_2 | g5442 | g5442.t1 | isoform | g5442.t1 | 9599032 | 9601666 |
| chr_2 | g5442 | g5442.t1 | exon | g5442.t1.exon1 | 9599032 | 9599912 |
| chr_2 | g5442 | g5442.t1 | cds | g5442.t1.CDS1 | 9599032 | 9599912 |
| chr_2 | g5442 | g5442.t1 | exon | g5442.t1.exon2 | 9601222 | 9601666 |
| chr_2 | g5442 | g5442.t1 | cds | g5442.t1.CDS2 | 9601222 | 9601666 |
| chr_2 | g5442 | g5442.t1 | TSS | g5442.t1 | NA | NA |
Sequences
>g5442.t1 Gene=g5442 Length=1326
ATGCGAAATTTTCTTTTTGTTGTTGCGGTGCTGGCGACATTATTAAATGGACAATTAGTC
GCTAGCACCGAGGAAGTAAAGTCTTCTTCATTAATATTTAAATCATCGTTAGTATCATCA
TCAATATCATCATCGCCTTCAGAATCAGATTCCTCATTATTAGACAGTAGAAATAGTATA
AGCTTAAGTAATAGAATAGAAAATGAGCATGGTAGAGGTAATAAGCCTGATCCTCAAACG
CTAGTCCAAATTGAGAAAAATCTCCTGTCATTATTTGGTTTCGAAAAGAGACCGAAAGTC
GACAGGTCAAAAATTGTGATCCCAGAAGCTATGAAGAAACTCTATGCCCAAATAATGGGA
CATGAATTAGAGACAGATCTAGAAGCACCAAAGGCAGATTTATTTAACAAAGAAGCCAAT
ACTGTAAGGAGCTACACTCATGAAGAAAGTAATGTGGATAATCGCTTTAAATATCATAAT
AGATTTCGACTCTTCTTCAATGTCTCAAATATACCAGAAAAAGAACGATTAAGGGATGCT
GAAATAACATTCAATCGCAACCAAATTAAAAACGTAAATAATATAAGGCATCAAATTGAT
GTTTACGATATTTTACGTCCAGGACGTAAACACAAAAAGCGTAAGCCTATATTTCGCTTA
ACTGCTTCGCGAGTAGTTAATATCAATGAGACTGGAAGCATCAGTTTAAACGTGATGTCA
GCGGTAAAGCGGTGGCTACGCGAACCTAAGCGTAATCATGGCATGTTAGTTCACATATCA
GCATTAGATGATAGAAGTAACTCAATTAACATCGATGACTCTTTTATTGTGCCATCACAT
GAACATATTAGACTTAAGAGAAGCATAGACGATAGTCCTGAAAATTGGGCGCAAGCTCAA
CCACTACTTTTCACTTATACAGATGATGGTCGATATAAACAGCGATCAATACGTGATGCA
AATCGTTCAAGACGAGCGCCTGGTAAAGGTAAAAGAAGAAAACAAAACCATGACGTTTGT
CAGCGACGGCCACTATATGTTGACTTTAGTGACGTTGGATGGAATGATTGGATTGTTGCA
CCACCAGGATATGAAGCATTTTATTGTCATGGAGAATGTAATTTTCCAATTGCTGATCAT
CTCAATACAACAAATCATGCTATTGTACAAACCCTTGTTCATTCAATTAATTCTAATCTT
GCACCAAAGGCATGTTGCGTGCCTACACAATTATCATCAATATCAATGCTCTATTTAGAT
GATCAGAATAAAGTTGTGCTTAAAAATTATCAAGACATGACAGTTGTAGGCTGTGGTTGT
AGATGA
>g5442.t1 Gene=g5442 Length=441
MRNFLFVVAVLATLLNGQLVASTEEVKSSSLIFKSSLVSSSISSSPSESDSSLLDSRNSI
SLSNRIENEHGRGNKPDPQTLVQIEKNLLSLFGFEKRPKVDRSKIVIPEAMKKLYAQIMG
HELETDLEAPKADLFNKEANTVRSYTHEESNVDNRFKYHNRFRLFFNVSNIPEKERLRDA
EITFNRNQIKNVNNIRHQIDVYDILRPGRKHKKRKPIFRLTASRVVNINETGSISLNVMS
AVKRWLREPKRNHGMLVHISALDDRSNSINIDDSFIVPSHEHIRLKRSIDDSPENWAQAQ
PLLFTYTDDGRYKQRSIRDANRSRRAPGKGKRRKQNHDVCQRRPLYVDFSDVGWNDWIVA
PPGYEAFYCHGECNFPIADHLNTTNHAIVQTLVHSINSNLAPKACCVPTQLSSISMLYLD
DQNKVVLKNYQDMTVVGCGCR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5442.t1 | CDD | cd13760 | TGF_beta_BMP2_like | 340 | 441 | 3.1439E-74 |
| 11 | g5442.t1 | Gene3D | G3DSA:2.60.120.970 | - | 80 | 292 | 2.7E-10 |
| 10 | g5442.t1 | Gene3D | G3DSA:2.10.90.10 | - | 327 | 441 | 1.8E-43 |
| 21 | g5442.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 315 | 337 | - |
| 3 | g5442.t1 | PANTHER | PTHR11848:SF54 | PROTEIN DECAPENTAPLEGIC | 29 | 441 | 5.5E-122 |
| 4 | g5442.t1 | PANTHER | PTHR11848 | TGF-BETA FAMILY | 29 | 441 | 5.5E-122 |
| 6 | g5442.t1 | PRINTS | PR00669 | Inhibin alpha chain signature | 340 | 357 | 9.7E-6 |
| 5 | g5442.t1 | PRINTS | PR00669 | Inhibin alpha chain signature | 357 | 374 | 9.7E-6 |
| 1 | g5442.t1 | Pfam | PF00688 | TGF-beta propeptide | 78 | 306 | 7.1E-33 |
| 2 | g5442.t1 | Pfam | PF00019 | Transforming growth factor beta like domain | 340 | 440 | 2.7E-33 |
| 13 | g5442.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 14 | g5442.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 15 | g5442.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 16 | g5442.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 23 | - |
| 12 | g5442.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 441 | - |
| 20 | g5442.t1 | ProSitePatterns | PS00250 | TGF-beta family signature. | 358 | 373 | - |
| 22 | g5442.t1 | ProSiteProfiles | PS51362 | TGF-beta family profile. | 322 | 441 | 44.598 |
| 19 | g5442.t1 | SMART | SM00204 | TGFB_2 | 340 | 441 | 3.3E-66 |
| 7 | g5442.t1 | SUPERFAMILY | SSF57501 | Cystine-knot cytokines | 333 | 441 | 9.03E-42 |
| 9 | g5442.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
| 18 | g5442.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 8 | g5442.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5442/g5442.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5442.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008083 | growth factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04662 (bone morphogenetic protein 4)
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.
