General information for g9946.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein trunk.
Parent gene
- The parent gene g9946 is located on chr_1: 6133069..6133915 (- 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 | g9946 | g9946.t1 | isoform | g9946.t1 | 6133069 | 6133915 |
| chr_1 | g9946 | g9946.t1 | exon | g9946.t1.exon1 | 6133069 | 6133654 |
| chr_1 | g9946 | g9946.t1 | cds | g9946.t1.CDS1 | 6133069 | 6133654 |
| chr_1 | g9946 | g9946.t1 | exon | g9946.t1.exon2 | 6133725 | 6133915 |
| chr_1 | g9946 | g9946.t1 | cds | g9946.t1.CDS2 | 6133725 | 6133915 |
| chr_1 | g9946 | g9946.t1 | TSS | g9946.t1 | NA | NA |
| chr_1 | g9946 | g9946.t1 | TTS | g9946.t1 | NA | NA |
Sequences
>g9946.t1 Gene=g9946 Length=777
ATGGTGCAAATTAAATTTACAATTATGCTTATATTTTTAAGTTTATCATGGACAATTAAT
GCAAAAGTTACTTTTAATAGAATGATATTAAATGAGAAAAGTAGACAAAATGATGAAGCT
ATAGTGAAACGATGTGATGAACTATCGCCAATAATGCTTAACGATATTTTGGGAGCTGCT
TATAATTCAAGGTATATGAGCATTGAAGAGCCAAAATTAGAGGAGGAATTAGAGCAGAAA
AATGCAGCCGGTAAGCGTGGAGCGCAAGACTTTCAACCGTTTTATGTTGATGACACATAT
GCAATGGAAATAAGTGATATGCCAGCATGGGAAGTTCATCATCCTGTGAACTCAACTGAG
AAGAATAATACTACATCAGAATCTGAAATGACGACAACAATGAAGAACAATGGACAACGA
GTAGTACGATCAAATAAAAGACGACGTACAGAAGATTTCAACAGTGGATATCAACCGCCA
CCTCCACAAAATAAAAGACCATGGGAATGTGAGGCAAAAATAAAGTGGTTAGACCTCGGT
CATGATTACTATCCAAGATATCTGCGAACTGTCGAGTGTACACGTCATTCATGTTTCTAT
GGACATTTCACTTGCAAACCAAGATCATTTACTGTTAAAATTCTTCGACGACGAAAAGGG
GAATGCGTGCAAACAAGAAATAGAGTCGGAATTAGCGGTTTGCCTGGTGAACTCAAAGAA
CTTTGGGTTTGGGAGGAGAGAGCTGTAAATTTTTGCTGCGACTGTGCGGTAAAATAA
>g9946.t1 Gene=g9946 Length=258
MVQIKFTIMLIFLSLSWTINAKVTFNRMILNEKSRQNDEAIVKRCDELSPIMLNDILGAA
YNSRYMSIEEPKLEEELEQKNAAGKRGAQDFQPFYVDDTYAMEISDMPAWEVHHPVNSTE
KNNTTSESEMTTTMKNNGQRVVRSNKRRRTEDFNSGYQPPPPQNKRPWECEAKIKWLDLG
HDYYPRYLRTVECTRHSCFYGHFTCKPRSFTVKILRRRKGECVQTRNRVGISGLPGELKE
LWVWEERAVNFCCDCAVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9946.t1 | Gene3D | G3DSA:2.10.90.10 | - | 37 | 216 | 1.2E-7 |
| 8 | g9946.t1 | Gene3D | G3DSA:1.10.287.520 | Helix hairpin bin | 76 | 169 | 1.2E-7 |
| 4 | g9946.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 164 | - |
| 5 | g9946.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 140 | - |
| 1 | g9946.t1 | PANTHER | PTHR39940 | PROTHORACICOTROPIC HORMONE, ISOFORM F | 5 | 257 | 2.2E-78 |
| 2 | g9946.t1 | PANTHER | PTHR39940:SF4 | PROTEIN TRUNK | 5 | 257 | 2.2E-78 |
| 10 | g9946.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 11 | g9946.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 12 | g9946.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 16 | - |
| 13 | g9946.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 9 | g9946.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 258 | - |
| 3 | g9946.t1 | SUPERFAMILY | SSF57501 | Cystine-knot cytokines | 41 | 245 | 5.42E-23 |
| 6 | g9946.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K20226 (protein trunk)
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.
