General information for g17000.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Brachyurin.
Parent gene
- The parent gene g17000 is located on chr_4: 12005435..12006949 (- 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 | g17000 | g17000.t1 | TTS | g17000.t1 | 12004846 | 12004846 |
| chr_4 | g17000 | g17000.t1 | isoform | g17000.t1 | 12004876 | 12006949 |
| chr_4 | g17000 | g17000.t1 | exon | g17000.t1.exon1 | 12004876 | 12004946 |
| chr_4 | g17000 | g17000.t1 | cds | g17000.t1.CDS1 | 12004876 | 12004946 |
| chr_4 | g17000 | g17000.t1 | exon | g17000.t1.exon2 | 12005137 | 12005250 |
| chr_4 | g17000 | g17000.t1 | cds | g17000.t1.CDS2 | 12005137 | 12005250 |
| chr_4 | g17000 | g17000.t1 | exon | g17000.t1.exon3 | 12005430 | 12005582 |
| chr_4 | g17000 | g17000.t1 | cds | g17000.t1.CDS3 | 12005430 | 12005582 |
| chr_4 | g17000 | g17000.t1 | exon | g17000.t1.exon4 | 12005663 | 12005808 |
| chr_4 | g17000 | g17000.t1 | cds | g17000.t1.CDS4 | 12005663 | 12005808 |
| chr_4 | g17000 | g17000.t1 | exon | g17000.t1.exon5 | 12005869 | 12005995 |
| chr_4 | g17000 | g17000.t1 | cds | g17000.t1.CDS5 | 12005869 | 12005995 |
| chr_4 | g17000 | g17000.t1 | exon | g17000.t1.exon6 | 12006058 | 12006098 |
| chr_4 | g17000 | g17000.t1 | cds | g17000.t1.CDS6 | 12006058 | 12006098 |
| chr_4 | g17000 | g17000.t1 | exon | g17000.t1.exon7 | 12006696 | 12006949 |
| chr_4 | g17000 | g17000.t1 | cds | g17000.t1.CDS7 | 12006696 | 12006949 |
| chr_4 | g17000 | g17000.t1 | TSS | g17000.t1 | 12006969 | 12006969 |
Sequences
>g17000.t1 Gene=g17000 Length=906
ATGAAATTTTTCATTTTCTTGGCTCTTTTGTTAACATCAGCAGCAGTTTTTGCTGACAAT
TATGATGAAATTGATTGGTCGCGAGTAATGCCACGCGAAGATGAGCCAGGTTTTTGGGAT
GATCGTGATGAAAATTTAAAACCATTGCCAGTTGATGTTCGATCAAGAAGAATCATTGGA
GGTTGGGAAGTTGAACGAAATAGTCATCCTTATGCAGTGTTTTTGCTTATGACTTCTGGA
TCTAGCTCTTTTAGGTGTGGAGCTTCAATAATCAGCAGCAGAGCTGTTTTGACAGCTGCA
CATTGTCCAAGTGGAACTTCATCAACATTAGCAATCACTGGTGCTCATAATGTTCAACAA
GTTGAACCAACACAACAAAGACGTACAATTCCATCATCAGCTTATCGTCTTCATGCTAAT
TACAATCCTTCAACTTTACAAAATGACATTGCAATTTTGATTACACCAACTGATGTTATT
GAAACCCAATATGTCCGTTTTTCACGACTTCCTCATGATTTTAGAAATGAACTTTTTACT
GGTGAACTTGTTTCAATTGTTGGATGGGGTCGAACTTGTGTGACATGTCCTGGTTCTGAT
GTTCTTCGTGGTGTTCAAAATTACATTATTTCTAATGCTGAATGTCGTGCTATTTATGGA
AATACTGTAACTGATTTGTTCTTCTGTATGCAAACAACTGGTCAAAGAGGAACATGCCCA
GGTGACTCAGGCGGACCATATACACTTCCCAGACCAGGACCTAGCGATCAATTGCCAGTA
ATTCAAATCGGTGTGCATTCATTTGGTGCTTCTACTGCAGTAGGAGGTTGCGAAGCTCAA
AGACCAAGTGGTGCAAGCAGAACAACAGCTTTCTTGGATTGGATTGCAGTAAATATGGTT
CCATAA
>g17000.t1 Gene=g17000 Length=301
MKFFIFLALLLTSAAVFADNYDEIDWSRVMPREDEPGFWDDRDENLKPLPVDVRSRRIIG
GWEVERNSHPYAVFLLMTSGSSSFRCGASIISSRAVLTAAHCPSGTSSTLAITGAHNVQQ
VEPTQQRRTIPSSAYRLHANYNPSTLQNDIAILITPTDVIETQYVRFSRLPHDFRNELFT
GELVSIVGWGRTCVTCPGSDVLRGVQNYIISNAECRAIYGNTVTDLFFCMQTTGQRGTCP
GDSGGPYTLPRPGPSDQLPVIQIGVHSFGASTAVGGCEAQRPSGASRTTAFLDWIAVNMV
P
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g17000.t1 | CDD | cd00190 | Tryp_SPc | 58 | 295 | 7.56367E-58 |
| 9 | g17000.t1 | Gene3D | G3DSA:2.40.10.10 | - | 52 | 299 | 8.2E-50 |
| 2 | g17000.t1 | PANTHER | PTHR24250:SF56 | SERINE PROTEASE P96 | 6 | 297 | 8.9E-61 |
| 3 | g17000.t1 | PANTHER | PTHR24250 | CHYMOTRYPSIN-RELATED | 6 | 297 | 8.9E-61 |
| 6 | g17000.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 87 | 102 | 1.2E-9 |
| 4 | g17000.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 145 | 159 | 1.2E-9 |
| 5 | g17000.t1 | PRINTS | PR00722 | Chymotrypsin serine protease family (S1) signature | 236 | 248 | 1.2E-9 |
| 1 | g17000.t1 | Pfam | PF00089 | Trypsin | 58 | 295 | 2.7E-45 |
| 11 | g17000.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 12 | g17000.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 13 | g17000.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 14 | g17000.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 10 | g17000.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 301 | - |
| 18 | g17000.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 97 | 102 | - |
| 19 | g17000.t1 | ProSitePatterns | PS00135 | Serine proteases, trypsin family, serine active site. | 237 | 248 | - |
| 20 | g17000.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 58 | 300 | 23.725 |
| 17 | g17000.t1 | SMART | SM00020 | trypsin_2 | 57 | 295 | 2.2E-51 |
| 7 | g17000.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 50 | 296 | 1.24E-59 |
| 8 | g17000.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 16 | g17000.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
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