General information for g13568.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein 60A.
Parent gene
- The parent gene g13568 is located on chr_1: 30962254..30963160 (- 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 | g13568 | g13568.t2 | TTS | g13568.t2 | 30959821 | 30959821 |
| chr_1 | g13568 | g13568.t2 | isoform | g13568.t2 | 30960024 | 30961020 |
| chr_1 | g13568 | g13568.t2 | exon | g13568.t2.exon1 | 30960024 | 30960149 |
| chr_1 | g13568 | g13568.t2 | cds | g13568.t2.CDS1 | 30960024 | 30960149 |
| chr_1 | g13568 | g13568.t2 | exon | g13568.t2.exon2 | 30960208 | 30960525 |
| chr_1 | g13568 | g13568.t2 | cds | g13568.t2.CDS2 | 30960208 | 30960525 |
| chr_1 | g13568 | g13568.t2 | exon | g13568.t2.exon3 | 30960775 | 30961020 |
| chr_1 | g13568 | g13568.t2 | cds | g13568.t2.CDS3 | 30960775 | 30960909 |
| chr_1 | g13568 | g13568.t2 | TSS | g13568.t2 | NA | NA |
Sequences
>g13568.t2 Gene=g13568 Length=690
GAAGACTTAAAACTGCTCTCATTTGTGAACACAACCACGCACACTGACGGTTGGCTTGAG
TTAAATGTTACACTCGCATTAAAAGAGTGGATTGAGCAAAGTGCAAGTAATATGGGATTT
GTGATAAAAGCAAATTTAATTGAAAGACCAGATAAAGATTTAAGGCTTGATGATATTGGA
CTTGTCAGCTCACGTGGTGATGATGAATTTCAACCTTTTATGGTTGGATTTTTCAAAGGA
CAAGAAATGATAAAACCGAAGAAAACAACAAAACATCATCACACAAGAACAAAGAGACAA
GCAAATCACAGAACTAAAAGCAAAAGAAAGTCAGATAATCGAAATCCATTTCTATCGCCG
GGTGAAAACAATCCAAAATCGTGCCAGATTAAAAATCTCTATGTGAGTTTCAAGGACTTA
AAATGGCAAGACTGGATCATTGCACCAGATGGATATGGAGCTTTTTATTGCGATGGCGAA
TGTAATTTTCCACTTAACGCCCATATGAACGCAAGTAATCATGCAATTGTTCAAACACTA
GTTCATCTAATGCATCCGACAAAGGTGCCAAAACCATGTTGTGCACCAACAAAATTAAGT
GCGATATCTGTTCTTTACTATCTTGATGATTCAAACGTAAATTTGAAAAAATACAAAAAT
ATGGTTGTAAAAAGTTGCGGATGCCATTAA
>g13568.t2 Gene=g13568 Length=192
MGFVIKANLIERPDKDLRLDDIGLVSSRGDDEFQPFMVGFFKGQEMIKPKKTTKHHHTRT
KRQANHRTKSKRKSDNRNPFLSPGENNPKSCQIKNLYVSFKDLKWQDWIIAPDGYGAFYC
DGECNFPLNAHMNASNHAIVQTLVHLMHPTKVPKPCCAPTKLSAISVLYYLDDSNVNLKK
YKNMVVKSCGCH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13568.t2 | CDD | cd13761 | TGF_beta_BMP5_like | 90 | 192 | 8.08629E-73 |
| 5 | g13568.t2 | Gene3D | G3DSA:2.10.90.10 | - | 81 | 192 | 2.2E-44 |
| 9 | g13568.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 48 | 85 | - |
| 10 | g13568.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 49 | 73 | - |
| 2 | g13568.t2 | PANTHER | PTHR11848:SF263 | DAWDLE, ISOFORM A-RELATED | 16 | 192 | 3.6E-76 |
| 3 | g13568.t2 | PANTHER | PTHR11848 | TGF-BETA FAMILY | 16 | 192 | 3.6E-76 |
| 1 | g13568.t2 | Pfam | PF00019 | Transforming growth factor beta like domain | 90 | 191 | 1.9E-36 |
| 7 | g13568.t2 | ProSitePatterns | PS00250 | TGF-beta family signature. | 109 | 124 | - |
| 11 | g13568.t2 | ProSiteProfiles | PS51362 | TGF-beta family profile. | 59 | 192 | 42.737 |
| 8 | g13568.t2 | SMART | SM00204 | TGFB_2 | 91 | 192 | 3.1E-65 |
| 4 | g13568.t2 | SUPERFAMILY | SSF57501 | Cystine-knot cytokines | 85 | 191 | 4.51E-41 |
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:0008083 | growth factor 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.
