General information for g3107.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein hedgehog.
Parent gene
- The parent gene g3107 is located on chr_3: 22827665..22840818 (- 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_3 | g3107 | g3107.t1 | isoform | g3107.t1 | 22827665 | 22840818 |
| chr_3 | g3107 | g3107.t1 | exon | g3107.t1.exon1 | 22827665 | 22828332 |
| chr_3 | g3107 | g3107.t1 | cds | g3107.t1.CDS1 | 22827665 | 22828332 |
| chr_3 | g3107 | g3107.t1 | exon | g3107.t1.exon2 | 22831700 | 22831961 |
| chr_3 | g3107 | g3107.t1 | cds | g3107.t1.CDS2 | 22831700 | 22831961 |
| chr_3 | g3107 | g3107.t1 | exon | g3107.t1.exon3 | 22840540 | 22840818 |
| chr_3 | g3107 | g3107.t1 | cds | g3107.t1.CDS3 | 22840540 | 22840818 |
| chr_3 | g3107 | g3107.t1 | TSS | g3107.t1 | 22841208 | 22841208 |
| chr_3 | g3107 | g3107.t1 | TTS | g3107.t1 | NA | NA |
Sequences
>g3107.t1 Gene=g3107 Length=1209
ATGAAGTCAATTTTTCTAATATTACTGCTGACAGTTAATACAGTGTTCTCATGCAGTCCC
ATACGAGGCATGGGTTCAAGAAAAAGTAGAAAATTAACGCCATTAGTATTCAAGCAGCAT
GTGCCAAATGTACTTGAAAATACACTCGGTGCGTCGGGTCTACATGAGGGTAAAATATCT
CGCGAAGATGCACGTTTCAAAGACCTTATACCGAATTATAATAAGGATATCATATTCAAA
GATGAAGAAGGAACTGGTGCTGATCGACTCATGACTCAGCGTTTGAAGGAGAAATTGAAT
ATATTAGCGATATCAGTAATGAATCAGTGGCCAAGTGTTAAACTTCGAGTCACGGAAGGC
TGGGATGAGGATGATTATCATTCAATCGACTCACTACATTACGAAGGTAGAGCAGTCGAT
ATAACGACATCAGATCGTGATCGTACGAAATATGGAATGCTTGCAAGATTAGCTGTTGAA
GCTGGATTTGATTGGGTTTACTACGAAAGTCGAGCGCACATTCATTGCTCAGTGAAGTCA
GATTCATCACAAGCTTCACATTCAAGTGGATGCTTCTCATTAGATAGCACAGTTGAGACT
GAAGATGGTAAAAGAAAATCATTAGCAGATTTACAGCTGGGTGAGCGTGTGCTTAGTGTC
AATAGCAATGGTGAGACAGTCTTTAGTGAAGTCATCATGTTTCTCGATCGCGAAATCAAT
CAGACACGAGAATTTGTGCAAATTAAAACAGATGGTGGTGCATTGCTTCGTCTAACACCT
GCACATTTGTTGCTACTTTGGAAGCCGCATTCACATGAAACCAAATACTTGTATGCAGAT
CAAGTGGAAGAGAATGATTTCCTTTTAGTCAATGTCAATGGTAATTTAGAACCACAGCGG
GTAACGGAAGTAAGAGCTGTGTTATCGAGGGGTTTCGTTGCACCATTGACACGGGAAGGA
ACGGTTGTAGTGAATGATGTTGCGGCATCATGTTATGCATTAGTTAATAGTCAAACTTTA
GCTCATATTAGTTTTATGCCATTTAGAACATTTAAGACAATTGAACATTGGTTCAATAGT
GGTAGAAATCAAAACAGTATAGATAGTAAATCGATTAGTAAACAAAATGGCATTCATTGG
TATGCAAATGCATTATATAAAGTTAAAGACTTTGTCCTACCTGACAAATATCTTTATTAT
AAAAAATAG
>g3107.t1 Gene=g3107 Length=402
MKSIFLILLLTVNTVFSCSPIRGMGSRKSRKLTPLVFKQHVPNVLENTLGASGLHEGKIS
REDARFKDLIPNYNKDIIFKDEEGTGADRLMTQRLKEKLNILAISVMNQWPSVKLRVTEG
WDEDDYHSIDSLHYEGRAVDITTSDRDRTKYGMLARLAVEAGFDWVYYESRAHIHCSVKS
DSSQASHSSGCFSLDSTVETEDGKRKSLADLQLGERVLSVNSNGETVFSEVIMFLDREIN
QTREFVQIKTDGGALLRLTPAHLLLLWKPHSHETKYLYADQVEENDFLLVNVNGNLEPQR
VTEVRAVLSRGFVAPLTREGTVVVNDVAASCYALVNSQTLAHISFMPFRTFKTIEHWFNS
GRNQNSIDSKSISKQNGIHWYANALYKVKDFVLPDKYLYYKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g3107.t1 | CDD | cd00081 | Hint | 191 | 331 | 6.9623E-26 |
| 17 | g3107.t1 | Gene3D | G3DSA:3.30.1380.10 | - | 15 | 181 | 1.6E-80 |
| 18 | g3107.t1 | Gene3D | G3DSA:2.170.16.10 | Hedgehog/intein (Hint) domain | 191 | 333 | 2.5E-43 |
| 3 | g3107.t1 | PANTHER | PTHR11889:SF39 | INDIAN HEDGEHOG PROTEIN | 4 | 396 | 6.5E-152 |
| 4 | g3107.t1 | PANTHER | PTHR11889 | HEDGEHOG | 4 | 396 | 6.5E-152 |
| 24 | g3107.t1 | PIRSF | PIRSF009400 | Hedgehog | 1 | 401 | 3.5E-180 |
| 10 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 90 | 108 | 5.7E-76 |
| 9 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 110 | 127 | 5.7E-76 |
| 8 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 130 | 152 | 5.7E-76 |
| 6 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 154 | 175 | 5.7E-76 |
| 12 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 176 | 194 | 5.7E-76 |
| 5 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 258 | 268 | 5.7E-76 |
| 7 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 311 | 325 | 5.7E-76 |
| 13 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 327 | 350 | 5.7E-76 |
| 11 | g3107.t1 | PRINTS | PR00632 | Sonic hedgehog protein signature | 377 | 393 | 5.7E-76 |
| 2 | g3107.t1 | Pfam | PF01085 | Hedgehog amino-terminal signalling domain | 18 | 177 | 2.0E-82 |
| 1 | g3107.t1 | Pfam | PF01079 | Hint module | 180 | 393 | 4.0E-69 |
| 20 | g3107.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 21 | g3107.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 22 | g3107.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 23 | g3107.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 19 | g3107.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 402 | - |
| 29 | g3107.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 18 | 5.0 |
| 28 | g3107.t1 | ProSiteProfiles | PS50817 | Intein N-terminal splicing motif profile. | 191 | 266 | 11.417 |
| 27 | g3107.t1 | SMART | SM00306 | hint_7 | 189 | 292 | 9.7E-23 |
| 26 | g3107.t1 | SMART | SM00305 | HINTC_6 | 293 | 337 | 3.0E-5 |
| 14 | g3107.t1 | SUPERFAMILY | SSF55166 | Hedgehog/DD-peptidase | 31 | 186 | 5.69E-79 |
| 15 | g3107.t1 | SUPERFAMILY | SSF51294 | Hedgehog/intein (Hint) domain | 191 | 333 | 1.27E-39 |
| 16 | g3107.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
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:0016540 | protein autoprocessing | BP |
| GO:0016539 | intein-mediated protein splicing | BP |
| GO:0007275 | multicellular organism development | BP |
| GO:0007267 | cell-cell signaling | BP |
KEGG
Orthology
- This transcript has been annotated with K06224 (hedgehog)
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. There were no conditions that were differentially expressed