General information for g17188.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g17188 is located on chr_4: 12774362..12776386 (+ 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_4 | g17188 | g17188.t1 | TSS | g17188.t1 | 12773643 | 12773643 |
| chr_4 | g17188 | g17188.t1 | isoform | g17188.t1 | 12774362 | 12776386 |
| chr_4 | g17188 | g17188.t1 | exon | g17188.t1.exon1 | 12774362 | 12774440 |
| chr_4 | g17188 | g17188.t1 | cds | g17188.t1.CDS1 | 12774362 | 12774440 |
| chr_4 | g17188 | g17188.t1 | exon | g17188.t1.exon2 | 12774496 | 12774653 |
| chr_4 | g17188 | g17188.t1 | cds | g17188.t1.CDS2 | 12774496 | 12774653 |
| chr_4 | g17188 | g17188.t1 | exon | g17188.t1.exon3 | 12774865 | 12775445 |
| chr_4 | g17188 | g17188.t1 | cds | g17188.t1.CDS3 | 12774865 | 12775445 |
| chr_4 | g17188 | g17188.t1 | exon | g17188.t1.exon4 | 12775506 | 12775681 |
| chr_4 | g17188 | g17188.t1 | cds | g17188.t1.CDS4 | 12775506 | 12775681 |
| chr_4 | g17188 | g17188.t1 | exon | g17188.t1.exon5 | 12776265 | 12776386 |
| chr_4 | g17188 | g17188.t1 | cds | g17188.t1.CDS5 | 12776265 | 12776386 |
| chr_4 | g17188 | g17188.t1 | TTS | g17188.t1 | 12776635 | 12776635 |
Sequences
>g17188.t1 Gene=g17188 Length=1116
ATGACTAAACGGATGATTGAAATTATTTTCTTAATTTTATTATGGATGAAAATGAATTCA
AATGTTATGGCCTCGAATGAAACGTCAAATTGTAGAGTAAAAGATGTTTATGTTGAAAAA
GGACAAAATTTTAACACTGTTTGTGAATGTTTAGGAGATTCAATCACTCAAATGTCATGG
TCATTTCAAAATTGTTCAAATTTACTATTTTCACCAGATTTTTGTCAAGGAATAAATACA
ACTGGAGATTTTCAATCTGAAAATTTGATAAAATTGGAAAATTCTTTGCTTATGCCAATC
AAATTTAATACAATGCAACCAGGAGTTATCACTTGTAAAGCATCAGGAAACTCTAAGGAT
GAAATAGTTCAAGGTTTTGTAAAAGTTATTGATTTACCAAAACCATTTGTATTAACTGGT
TTTAGTGAAAGTCATAAAATTGCTATTGGTGATTTTGTTGAACTTGAATGTGGTGCAGTA
AAATATGATTTTTCTAACTCAATTCAATGGATGAAAGATGGAAAACCAATAGGATATGGA
GAAGGAATTTTAATTAAAAATAGCAACACTGAATATTCATGGCGCAAAAAGTTAATTTTT
AATTCTATAAGTCATGAAAATGTAGGCAAATATGAATGTAAATCACAAAATATAAATACA
AAAGAGTTCAAAACATTATCAGTTAATATTAAAGTTTATGATCCAATTGATATTTCAATA
ACAACAAATTTCAATGAAACTACAATCACAAAAATTGTTGATGAAGTTTTAACACTTGAA
TGCAATGTTGATGGTATTCCAATGCCAACATTAATTTGGAAAAAAGATGACCAAATATTC
AATGTTAGTGAAAAAGACACAAGAGTGACAATGAAAAATCAAAACATGAATTTAACTTTT
GCAAGTCTTAGATTTAAAGACAGTGGAAAATATGAATGCATTGCACAAAATCGATTTGAA
AACGTTAGCAGAATATTTGAAGTCGTAATTGAAAAAGGACCAATTGATAAAAGAATCATT
ATTGGAGTCATCTGTGTTTTCATTGCACTCATATCGATATGCGCTTACTTGTACTACTCA
CGAAATAAAATTCCAGCTAAACGAGAAAATAACTAA
>g17188.t1 Gene=g17188 Length=371
MTKRMIEIIFLILLWMKMNSNVMASNETSNCRVKDVYVEKGQNFNTVCECLGDSITQMSW
SFQNCSNLLFSPDFCQGINTTGDFQSENLIKLENSLLMPIKFNTMQPGVITCKASGNSKD
EIVQGFVKVIDLPKPFVLTGFSESHKIAIGDFVELECGAVKYDFSNSIQWMKDGKPIGYG
EGILIKNSNTEYSWRKKLIFNSISHENVGKYECKSQNINTKEFKTLSVNIKVYDPIDISI
TTNFNETTITKIVDEVLTLECNVDGIPMPTLIWKKDDQIFNVSEKDTRVTMKNQNMNLTF
ASLRFKDSGKYECIAQNRFENVSRIFEVVIEKGPIDKRIIIGVICVFIALISICAYLYYS
RNKIPAKRENN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g17188.t1 | CDD | cd00096 | Ig | 153 | 225 | 3.93203E-4 |
| 22 | g17188.t1 | CDD | cd00096 | Ig | 257 | 327 | 1.88136E-12 |
| 11 | g17188.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 140 | 232 | 6.4E-10 |
| 12 | g17188.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 237 | 332 | 1.0E-17 |
| 3 | g17188.t1 | PANTHER | PTHR44427 | CARCINOEMBRYONIC ANTIGEN-RELATED CELL ADHESION MOLECULE 19 | 106 | 279 | 3.3E-22 |
| 5 | g17188.t1 | PANTHER | PTHR44427:SF18 | - | 106 | 279 | 3.3E-22 |
| 4 | g17188.t1 | PANTHER | PTHR44427 | CARCINOEMBRYONIC ANTIGEN-RELATED CELL ADHESION MOLECULE 19 | 208 | 329 | 3.3E-22 |
| 6 | g17188.t1 | PANTHER | PTHR44427:SF18 | - | 208 | 329 | 3.3E-22 |
| 20 | g17188.t1 | PIRSF | PIRSF000615 | TyrPK_CSF1-R | 13 | 365 | 5.5E-17 |
| 1 | g17188.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 140 | 230 | 3.6E-8 |
| 2 | g17188.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 251 | 329 | 8.6E-14 |
| 15 | g17188.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 24 | - |
| 16 | g17188.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 17 | g17188.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 16 | - |
| 19 | g17188.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 24 | - |
| 14 | g17188.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 25 | 338 | - |
| 18 | g17188.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 339 | 359 | - |
| 13 | g17188.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 360 | 371 | - |
| 28 | g17188.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 133 | 229 | 10.589 |
| 29 | g17188.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 235 | 323 | 11.098 |
| 25 | g17188.t1 | SMART | SM00409 | IG_3c | 142 | 231 | 2.8E-4 |
| 27 | g17188.t1 | SMART | SM00408 | igc2_5 | 148 | 220 | 2.4E-5 |
| 24 | g17188.t1 | SMART | SM00409 | IG_3c | 246 | 331 | 1.1E-5 |
| 26 | g17188.t1 | SMART | SM00408 | igc2_5 | 252 | 320 | 8.3E-8 |
| 8 | g17188.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 134 | 236 | 3.73E-12 |
| 7 | g17188.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 248 | 331 | 3.75E-16 |
| 10 | g17188.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
| 9 | g17188.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 24 | - |
| 23 | g17188.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 338 | 360 | - |
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 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