General information for g16607.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Brachyurin.
Parent gene
- The parent gene g16607 is located on chr_4: 10210960..10212665 (+ 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 | g16607 | g16607.t1 | TSS | g16607.t1 | 10210914 | 10210914 |
| chr_4 | g16607 | g16607.t1 | isoform | g16607.t1 | 10210960 | 10212665 |
| chr_4 | g16607 | g16607.t1 | exon | g16607.t1.exon1 | 10210960 | 10211094 |
| chr_4 | g16607 | g16607.t1 | cds | g16607.t1.CDS1 | 10210960 | 10211094 |
| chr_4 | g16607 | g16607.t1 | exon | g16607.t1.exon2 | 10211278 | 10211325 |
| chr_4 | g16607 | g16607.t1 | cds | g16607.t1.CDS2 | 10211278 | 10211325 |
| chr_4 | g16607 | g16607.t1 | exon | g16607.t1.exon3 | 10211937 | 10212387 |
| chr_4 | g16607 | g16607.t1 | cds | g16607.t1.CDS3 | 10211937 | 10212387 |
| chr_4 | g16607 | g16607.t1 | exon | g16607.t1.exon4 | 10212442 | 10212534 |
| chr_4 | g16607 | g16607.t1 | cds | g16607.t1.CDS4 | 10212442 | 10212534 |
| chr_4 | g16607 | g16607.t1 | exon | g16607.t1.exon5 | 10212604 | 10212665 |
| chr_4 | g16607 | g16607.t1 | cds | g16607.t1.CDS5 | 10212604 | 10212665 |
| chr_4 | g16607 | g16607.t1 | TTS | g16607.t1 | NA | NA |
Sequences
>g16607.t1 Gene=g16607 Length=789
ATGAAGATTTTGATTTTTGCTACTCTGATTTCGTTGACAAGTTGTTGGGTTAATTTGCCA
GATGAGGCAAAAACTGCAAAATCTATGGATGAACATCCAACGATTCAAAAGATTTTAAGA
GAAAAAAAATCCAGAATTTTTTATTGTGGTGGTTCATTGATTCGTTATAATTGGGTTTTG
ACAGCAGCTCATTGTGTTCTTGATCCTTTTATAAAATTAGCAGTCTACCTTGGTATCATT
GATTCTCGTTATGGACCTGCATATTGGGGTGCAGATGTGACTTTAAAATCAGATGTGAAA
GTTCATTCAAGTTACAACTATACCAATTTTGTTAATGATATTGCTATGATTTATTTAAGA
ACTGCAACTGAATCAATTTATAATGCTTATATTGGAACCATTCCATTGCCTAAAAGTCAT
GTCAATACAAATTTAGATGGAAGGAGTTCAATTGTGAGTGGTTTTGGCAGGACAAGTGAT
AACAGTACACAATCACAATTTTTGAAATATGTTCAACTCTATATTGCTTCAAATTCTGTT
TGTGAAGGCATTTATGGAACAAATGTTGTCAGAGATACAAACATTTGTGTTGCAACAACA
ACAACTGCAAGCACTTGCTCAGGAGATTCTGGAGGAGGATTGACCACTGTTCTTGATGGA
ACAAATTATGTTGTTGGAATCGTTTCGTTTGGTGCTGCTGCTTCATGTGAAATGGGCTAT
CCTGCTGGATTCACCCGAGTCACAAGTTATCTTGGATGGATTGACAATCAGTTCACAAGT
TTACCATAA
>g16607.t1 Gene=g16607 Length=262
MKILIFATLISLTSCWVNLPDEAKTAKSMDEHPTIQKILREKKSRIFYCGGSLIRYNWVL
TAAHCVLDPFIKLAVYLGIIDSRYGPAYWGADVTLKSDVKVHSSYNYTNFVNDIAMIYLR
TATESIYNAYIGTIPLPKSHVNTNLDGRSSIVSGFGRTSDNSTQSQFLKYVQLYIASNSV
CEGIYGTNVVRDTNICVATTTTASTCSGDSGGGLTTVLDGTNYVVGIVSFGAAASCEMGY
PAGFTRVTSYLGWIDNQFTSLP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g16607.t1 | CDD | cd00190 | Tryp_SPc | 47 | 257 | 4.30071E-49 |
| 9 | g16607.t1 | Gene3D | G3DSA:2.40.10.10 | - | 40 | 254 | 4.4E-52 |
| 10 | g16607.t1 | Gene3D | G3DSA:2.40.10.10 | - | 135 | 250 | 4.4E-52 |
| 2 | g16607.t1 | PANTHER | PTHR24260 | - | 30 | 259 | 3.9E-50 |
| 3 | g16607.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 50 | 65 | 1.8E-11 |
| 5 | g16607.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 109 | 123 | 1.8E-11 |
| 4 | g16607.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 203 | 215 | 1.8E-11 |
| 1 | g16607.t1 | Pfam | PF00089 | Trypsin | 31 | 254 | 5.2E-38 |
| 12 | g16607.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 15 | - |
| 13 | g16607.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 14 | g16607.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 10 | - |
| 15 | g16607.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 11 | 15 | - |
| 11 | g16607.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 16 | 262 | - |
| 18 | g16607.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 60 | 65 | - |
| 19 | g16607.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 15 | 5.0 |
| 20 | g16607.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 9 | 259 | 23.148 |
| 17 | g16607.t1 | SMART | SM00020 | trypsin_2 | 37 | 254 | 1.3E-42 |
| 6 | g16607.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 31 | 257 | 4.28E-55 |
| 8 | g16607.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 15 | - |
| 7 | g16607.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 23 | - |
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:0004252 | serine-type endopeptidase activity | MF |
| GO:0006508 | proteolysis | BP |
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