General information for g13260.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13260 is located on chr_1: 28844910..28845862 (+ 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 | g13260 | g13260.t2 | isoform | g13260.t2 | 28833011 | 28842657 |
| chr_1 | g13260 | g13260.t2 | exon | g13260.t2.exon1 | 28833011 | 28833060 |
| chr_1 | g13260 | g13260.t2 | TSS | g13260.t2 | 28833018 | 28833018 |
| chr_1 | g13260 | g13260.t2 | exon | g13260.t2.exon2 | 28833633 | 28833873 |
| chr_1 | g13260 | g13260.t2 | exon | g13260.t2.exon3 | 28837458 | 28837647 |
| chr_1 | g13260 | g13260.t2 | cds | g13260.t2.CDS1 | 28837536 | 28837647 |
| chr_1 | g13260 | g13260.t2 | exon | g13260.t2.exon4 | 28840991 | 28841044 |
| chr_1 | g13260 | g13260.t2 | cds | g13260.t2.CDS2 | 28840991 | 28841044 |
| chr_1 | g13260 | g13260.t2 | exon | g13260.t2.exon5 | 28841929 | 28841986 |
| chr_1 | g13260 | g13260.t2 | cds | g13260.t2.CDS3 | 28841929 | 28841986 |
| chr_1 | g13260 | g13260.t2 | exon | g13260.t2.exon6 | 28842055 | 28842345 |
| chr_1 | g13260 | g13260.t2 | cds | g13260.t2.CDS4 | 28842055 | 28842345 |
| chr_1 | g13260 | g13260.t2 | exon | g13260.t2.exon7 | 28842415 | 28842657 |
| chr_1 | g13260 | g13260.t2 | cds | g13260.t2.CDS5 | 28842415 | 28842655 |
| chr_1 | g13260 | g13260.t2 | TTS | g13260.t2 | NA | NA |
Sequences
>g13260.t2 Gene=g13260 Length=1127
TCAGTTTTAGTCTTCGTCGAGACGCTTTTCGAGTGAAAAGTCTAATTCGATTCTTTAGTT
CCCGTTTTAAAATTTTTTAAGTTCTTCAACCATTTTTTGAGTTTCCCGTTTTTAAACTGG
CATATAAAAAAGTTAAAATTGAAAAAAAGTCAAAGTGCAAGCTAAAGTCATTTTTAATGA
AAGAAACGGGAAATTTCATAAGCGAATTAAAGTGAAACTGAGAAAGAAAAGTTATTGTAA
TCGACATCAACACAAAAATGGGATTAATATGGTCAGAACATTCGTAGAGTGTAACGGCCA
CCAGACCATACCAATAGTTACAATAGTAGACAAACCCCATCAATTTGATTAAATCATCGA
AACACCGATATGTCAAATATTGACAAATGGATGAAATTATGGAAGGCACTGTTCTGTGGT
AGTTTCCTAATAACCATCATATGCGATCATCTTGGCACTGTTACGGGTCAAGAGAATATC
GGTTGCCTGTTTGCGGAGCAACTGTGTGTTCCACATCTAGAATGGTGCTTTGATGATTTT
GCATTTGGGAAATGTCTTCCATATTATGAATCAGATCCACAGCAATTTGAACGTGAGCCG
CTGACGCAAGAGCAAGTCTCTATATTAAAACAAATGCTGCAGGAGCTTCATGCTGCTGGT
CTTGACTGGGATCATCCGTTCACTCAATGTCGCATGCAGAATGCCATGTTTGCAATGCGA
AATCGAATCGATATGGAACGCGACGCTTGCGTGTCTTTGGCACCTCCACCAATCATTCCG
AAGTTTCTTGATCCAACCAATCCGCTCGCCTTCATACGATTCACACAGCCCATCATTGAT
CTTAACGATGAGTACATTTACCCGCCTTTGAAGAAATCTTACGAGTATGAAAATATCCCC
AAAACTCCACACCATCGACAACAACAACAACAGCCATCAATGGAGCAAATTCTATCATCA
CCTGACCAGTATGAATTTCTTCAACGCGAGTATAATGTACCACCATCAAATGAGATTATC
GATCCAGCAGTAGAGAACGAAATGCTGAATGTACTTGAGCGAACGAATGATTTACAGAAT
CGTATTAGCGACATCAAAAATCGTATGGAATTGCATCGAATGTTGGC
>g13260.t2 Gene=g13260 Length=252
MSNIDKWMKLWKALFCGSFLITIICDHLGTVTGQENIGCLFAEQLCVPHLEWCFDDFAFG
KCLPYYESDPQQFEREPLTQEQVSILKQMLQELHAAGLDWDHPFTQCRMQNAMFAMRNRI
DMERDACVSLAPPPIIPKFLDPTNPLAFIRFTQPIIDLNDEYIYPPLKKSYEYENIPKTP
HHRQQQQQPSMEQILSSPDQYEFLQREYNVPPSNEIIDPAVENEMLNVLERTNDLQNRIS
DIKNRMELHRML
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 1 | g13260.t2 | PANTHER | PTHR46106 | IA-2 PROTEIN TYROSINE PHOSPHATASE, ISOFORM C | 45 | 210 | 6.5E-22 |
| 2 | g13260.t2 | PANTHER | PTHR46106:SF4 | IA-2 PROTEIN TYROSINE PHOSPHATASE, ISOFORM C | 45 | 210 | 6.5E-22 |
| 5 | g13260.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 33 | - |
| 6 | g13260.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 12 | - |
| 7 | g13260.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 13 | 25 | - |
| 8 | g13260.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 26 | 33 | - |
| 4 | g13260.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 34 | 252 | - |
| 3 | g13260.t2 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 33 | - |
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:0030141 | secretory granule | CC |
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. There were no conditions that were differentially expressed