General information for g4405.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative cysteine proteinase CG12163.
Parent gene
- The parent gene g4405 is located on chr_2: 2005157..2008641 (- 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_2 | g4405 | g4405.t1 | TTS | g4405.t1 | 2001061 | 2001061 |
| chr_2 | g4405 | g4405.t1 | isoform | g4405.t1 | 2001294 | 2005157 |
| chr_2 | g4405 | g4405.t1 | exon | g4405.t1.exon1 | 2001294 | 2001377 |
| chr_2 | g4405 | g4405.t1 | cds | g4405.t1.CDS1 | 2001294 | 2001377 |
| chr_2 | g4405 | g4405.t1 | exon | g4405.t1.exon2 | 2001442 | 2001689 |
| chr_2 | g4405 | g4405.t1 | cds | g4405.t1.CDS2 | 2001442 | 2001689 |
| chr_2 | g4405 | g4405.t1 | exon | g4405.t1.exon3 | 2001757 | 2002007 |
| chr_2 | g4405 | g4405.t1 | cds | g4405.t1.CDS3 | 2001757 | 2002007 |
| chr_2 | g4405 | g4405.t1 | exon | g4405.t1.exon4 | 2002061 | 2003089 |
| chr_2 | g4405 | g4405.t1 | cds | g4405.t1.CDS4 | 2002061 | 2003089 |
| chr_2 | g4405 | g4405.t1 | exon | g4405.t1.exon5 | 2003160 | 2003281 |
| chr_2 | g4405 | g4405.t1 | cds | g4405.t1.CDS5 | 2003160 | 2003281 |
| chr_2 | g4405 | g4405.t1 | exon | g4405.t1.exon6 | 2003373 | 2004407 |
| chr_2 | g4405 | g4405.t1 | cds | g4405.t1.CDS6 | 2003373 | 2004407 |
| chr_2 | g4405 | g4405.t1 | exon | g4405.t1.exon7 | 2005077 | 2005157 |
| chr_2 | g4405 | g4405.t1 | cds | g4405.t1.CDS7 | 2005077 | 2005157 |
| chr_2 | g4405 | g4405.t1 | TSS | g4405.t1 | 2005223 | 2005223 |
Sequences
>g4405.t1 Gene=g4405 Length=2850
ATGTGGAAATTTAAAATTTTGCTAATTTGTTTAGCAAGTATTATAATAGTTAATGCCACA
GAATGTGAAGATTGTCAAAATGAGCCTCAATCTGAAGAACATTTTGTAGCCGTTCATGTG
AATCAAATGAATATCGTTTTGATTAATCCTGATTCTCCATTAATTGAAGAAATTGTTAGA
CCCTTTTTATCAAGCAAATTTAGTTTTCTCTATGCCATAAATGCCACACGAGAAATTGTC
AATGGTTTCAAATACGAAATTATTTTCACAATGTTAAGCACTGAAAATGGCATCGAGATT
TATTGCCTCATGGATGTTCTAGAAAAACCTTGGCTTATAAGCAATTACAAGAAATTTCGA
AAGATGACGTATAATAATTGTTCGTTAGAAAATCCATTAGACGAAGAAGATCGTATGCGA
TTTCAGTATGAAATAAATCCAACTTTTATTAATCAAAGAACTGAAATGAATGATGATGAC
ATTTCTGATATGGAGGATCAGATAATTACTGAAAGAGTTGTTGCTACAACAAATTCTATT
ACTTCATCATCATCAGATGATGTAACTTTAGATCCTTCATCTAAAACTCTTCTTGATGGA
TTTTTCAATACAAATAATTTTTTCCCTCAAACAACATCTACAACAACTATCAAACCGTTA
TCATTGGATCTATTAGATGAAATGTTTGGTGTCAGAAAAATCGAAAATTCTCAATCTCAA
CCGTCGACAGTGACGACAGATAATGCCGATGAACTGCAACAAAGAACTCAAGAAAATGAA
AAAAATTCCGATAATCAAGAAGATAGAGAAAATGACACGGCATTGAAGGGTCTCGAAATA
GAAATAAAGAAAACTTTTAGTGAGCTATTTCAAACTAATTCCGATTTTAGAATGAATATA
ATAGCGCTGATAAATAGAAAAGATGATTTGACTGCACAAAAGAATTACAACTATGTAGTC
AATATATTAGCAAGTAAACTTAAAGATAAAATTGAGTCATACAATGAGAGAAGATTTAAA
GATGAGCAAACTCAAAATAATTATCAGCAAATAAATACTAATAGAACAAAGCGCTCTTAC
TTTTTTGATTCCCAAAATTCCTTTCCATCTCACAAGCGTGCTGCTCGTCAAATCGGTGTT
CCCGGTGGAATCAGTCCTGTAGAAAACTTTGAAGATGTAAAAATTTATGTTCAAGAAGCT
ATTGATGAAATTAATGATAATGAAGATCCTGATTACATTTTGAAACATATCGTTGAAGCA
ACCCAACAAGTTGTTGCAGGCATGAGTTATAAAATTAAAGCAGTGTTTTCCAGAGATGGA
AGCGACATTGAATGTGATTTTGATGTATGGGAGCAAGCTTGGATTAAAGATGGACGTAAA
GTTTCAGTTTCTTGCAAAAATGATAAGAAATATAAGTTGACCCAATCACCATCTAATCAG
CGTGTCAAACGTGATAACACGCTTGAAAGAGTTCTTGGTTTACCATCCAATACTGATGAT
CATGACGATTTGATAAAAATACTTTCTGAACATTTGAAGAGACTCGATACTGGAAGTGAT
GCACAATTTGAATTGGTAAAACTTGAAAAGGTAACTCAACAAGTAGTAGCTGGAATAAAA
TATAAAGCAACAGGTATTTTTAAAATTGGCAATGAAGAGAAAAAATGTGTTATCGATGTA
TGGCATCGCTCATGGATTAAGGGAGATGAAGGCACTCAATTAAGCGCTGATTGTGATAAA
GGTGCAACAACTTTCAAGACAAAATCTTCTAGAAAAAGGAGATCAGTTCATCACCACACA
CACAATCGTCACAATAGACAATCAGTAAGCGATCATTTTGATGACCATCATCATCATACT
GATAGACATCATCATCAATACTCAGCTACTGAAGAAATGAAAGAAATAAAATCTGAAATT
TTATTTAACAATTTCATAACTAAATATAATCGTAAATATGCCAATGAACTTGAACATAAA
ATGAGAATGAGAATTTTCAAGAAGAATTTACATAAAATTGAAATGTTGAATAAGCATGAA
CAAGGCACTGCAAAGTATGGAATTACAGAATTCGCTGATTTAACTGAAAAGGAATACTTG
CATAAAACTGGTTTGAGAGTGCGTGAAAGACATGAGAATGAATTAGAAAATCCAATTGCA
CATATTCCAGAAGTTGAAGATTTACCAACCGAATTTGATTGGAGAGATAAATCAGCAGTT
ACAAGTGTAAAAAATCAAGGAAATTGTGGATCATGCTGGAGTTTTTCTGTTACAGGAAAT
ATTGAAGGCTTACATGCTATTAAAACTGGAAAACTTGAAGCTTATTCTGAACAAGAACTT
TTGGACTGTGATACAACTGATAATGCTTGCAATGGTGGTTATATGGATGATGCTTTTAAA
GCAATTGAAAAAATTGGTGGTCTAGAATTAGAAGATGAATATCCTTATCAAGCAAGGAAA
CAAAAGAAATGCTTGTTTAATGCTACTATGAGTCATGTTAAAGTTAAAGGTGTTGTAGAT
TTGCCTAAAGGTGATGAAATTGCAATGCAAAAGTTTTTAGTCTCAACTGGTCCGATTTCC
ATTGGCATAAATGCTAATGCTATGCAATTTTATCGTGGTGGTGTTTCGCATCCATGGAAA
GTTCTTTGCAGAAAATCTAATTTAGATCATGGTGTTTTGATTGTTGGATATGGAATAAAA
GAGTATCCCATGTTTAATAAAACTTTACCTTATTGGACTATTAAAAATTCATGGGGTCCA
AAATGGGGTGAACAAGGATATTATCGAGTTTATCGTGGAGATAACAGTTGTGGAGTTGCA
GAAATGGCAAGCAGCGCAGTACTTGAATAA
>g4405.t1 Gene=g4405 Length=949
MWKFKILLICLASIIIVNATECEDCQNEPQSEEHFVAVHVNQMNIVLINPDSPLIEEIVR
PFLSSKFSFLYAINATREIVNGFKYEIIFTMLSTENGIEIYCLMDVLEKPWLISNYKKFR
KMTYNNCSLENPLDEEDRMRFQYEINPTFINQRTEMNDDDISDMEDQIITERVVATTNSI
TSSSSDDVTLDPSSKTLLDGFFNTNNFFPQTTSTTTIKPLSLDLLDEMFGVRKIENSQSQ
PSTVTTDNADELQQRTQENEKNSDNQEDRENDTALKGLEIEIKKTFSELFQTNSDFRMNI
IALINRKDDLTAQKNYNYVVNILASKLKDKIESYNERRFKDEQTQNNYQQINTNRTKRSY
FFDSQNSFPSHKRAARQIGVPGGISPVENFEDVKIYVQEAIDEINDNEDPDYILKHIVEA
TQQVVAGMSYKIKAVFSRDGSDIECDFDVWEQAWIKDGRKVSVSCKNDKKYKLTQSPSNQ
RVKRDNTLERVLGLPSNTDDHDDLIKILSEHLKRLDTGSDAQFELVKLEKVTQQVVAGIK
YKATGIFKIGNEEKKCVIDVWHRSWIKGDEGTQLSADCDKGATTFKTKSSRKRRSVHHHT
HNRHNRQSVSDHFDDHHHHTDRHHHQYSATEEMKEIKSEILFNNFITKYNRKYANELEHK
MRMRIFKKNLHKIEMLNKHEQGTAKYGITEFADLTEKEYLHKTGLRVRERHENELENPIA
HIPEVEDLPTEFDWRDKSAVTSVKNQGNCGSCWSFSVTGNIEGLHAIKTGKLEAYSEQEL
LDCDTTDNACNGGYMDDAFKAIEKIGGLELEDEYPYQARKQKKCLFNATMSHVKVKGVVD
LPKGDEIAMQKFLVSTGPISIGINANAMQFYRGGVSHPWKVLCRKSNLDHGVLIVGYGIK
EYPMFNKTLPYWTIKNSWGPKWGEQGYYRVYRGDNSCGVAEMASSAVLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g4405.t1 | CDD | cd00042 | CY | 382 | 465 | 5.06908E-9 |
| 23 | g4405.t1 | CDD | cd02248 | Peptidase_C1A | 729 | 946 | 7.54697E-99 |
| 17 | g4405.t1 | Coils | Coil | Coil | 249 | 269 | - |
| 14 | g4405.t1 | Gene3D | G3DSA:3.10.450.10 | - | 376 | 469 | 9.2E-16 |
| 15 | g4405.t1 | Gene3D | G3DSA:3.10.450.10 | - | 488 | 577 | 1.7E-10 |
| 16 | g4405.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 608 | 948 | 4.1E-101 |
| 35 | g4405.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 584 | 630 | - |
| 33 | g4405.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 587 | 605 | - |
| 34 | g4405.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 606 | 630 | - |
| 4 | g4405.t1 | PANTHER | PTHR13814:SF16 | CYSTATIN | 641 | 947 | 7.3E-100 |
| 5 | g4405.t1 | PANTHER | PTHR13814 | FETUIN | 641 | 947 | 7.3E-100 |
| 8 | g4405.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 746 | 761 | 2.1E-8 |
| 7 | g4405.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 890 | 900 | 2.1E-8 |
| 6 | g4405.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 911 | 917 | 2.1E-8 |
| 2 | g4405.t1 | Pfam | PF00031 | Cystatin domain | 382 | 438 | 7.0E-6 |
| 1 | g4405.t1 | Pfam | PF08246 | Cathepsin propeptide inhibitor domain (I29) | 642 | 699 | 6.4E-12 |
| 3 | g4405.t1 | Pfam | PF00112 | Papain family cysteine protease | 728 | 946 | 6.2E-71 |
| 19 | g4405.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 20 | g4405.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 21 | g4405.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 17 | - |
| 22 | g4405.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 22 | - |
| 18 | g4405.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 949 | - |
| 32 | g4405.t1 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 746 | 757 | - |
| 31 | g4405.t1 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 888 | 898 | - |
| 30 | g4405.t1 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 911 | 930 | - |
| 29 | g4405.t1 | SMART | SM00043 | CY_4 | 379 | 466 | 7.0E-10 |
| 28 | g4405.t1 | SMART | SM00043 | CY_4 | 490 | 579 | 0.18 |
| 27 | g4405.t1 | SMART | SM00848 | Inhibitor_I29_2 | 642 | 699 | 3.0E-18 |
| 26 | g4405.t1 | SMART | SM00645 | pept_c1 | 728 | 947 | 2.0E-100 |
| 10 | g4405.t1 | SUPERFAMILY | SSF54403 | Cystatin/monellin | 377 | 468 | 2.98E-13 |
| 9 | g4405.t1 | SUPERFAMILY | SSF54403 | Cystatin/monellin | 500 | 567 | 7.87E-8 |
| 11 | g4405.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 635 | 946 | 1.12E-99 |
| 13 | g4405.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 25 | g4405.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 12 | g4405.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 25 | - |
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:0008234 | cysteine-type peptidase activity | MF |
| GO:0006508 | proteolysis | BP |
| GO:0004869 | cysteine-type endopeptidase inhibitor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01373 (cathepsin F)
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.
