General information for g16342.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cathepsin L.
Parent gene
- The parent gene g16342 is located on chr_4: 9138600..9142562 (- 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 | g16342 | g16342.t1 | isoform | g16342.t1 | 9138600 | 9142562 |
| chr_4 | g16342 | g16342.t1 | exon | g16342.t1.exon1 | 9138600 | 9138679 |
| chr_4 | g16342 | g16342.t1 | cds | g16342.t1.CDS1 | 9138600 | 9138679 |
| chr_4 | g16342 | g16342.t1 | exon | g16342.t1.exon2 | 9138815 | 9138827 |
| chr_4 | g16342 | g16342.t1 | cds | g16342.t1.CDS2 | 9138815 | 9138827 |
| chr_4 | g16342 | g16342.t1 | exon | g16342.t1.exon3 | 9138884 | 9139045 |
| chr_4 | g16342 | g16342.t1 | cds | g16342.t1.CDS3 | 9138884 | 9139045 |
| chr_4 | g16342 | g16342.t1 | exon | g16342.t1.exon4 | 9139113 | 9139425 |
| chr_4 | g16342 | g16342.t1 | cds | g16342.t1.CDS4 | 9139113 | 9139425 |
| chr_4 | g16342 | g16342.t1 | exon | g16342.t1.exon5 | 9139574 | 9139937 |
| chr_4 | g16342 | g16342.t1 | cds | g16342.t1.CDS5 | 9139574 | 9139937 |
| chr_4 | g16342 | g16342.t1 | exon | g16342.t1.exon6 | 9140919 | 9141001 |
| chr_4 | g16342 | g16342.t1 | cds | g16342.t1.CDS6 | 9140919 | 9141001 |
| chr_4 | g16342 | g16342.t1 | exon | g16342.t1.exon7 | 9141259 | 9142562 |
| chr_4 | g16342 | g16342.t1 | cds | g16342.t1.CDS7 | 9141259 | 9142562 |
| chr_4 | g16342 | g16342.t1 | TSS | g16342.t1 | NA | NA |
| chr_4 | g16342 | g16342.t1 | TTS | g16342.t1 | NA | NA |
Sequences
>g16342.t1 Gene=g16342 Length=2319
ATGTTTCAAACAGTTCTTGAAATTTTCTCAACATTTGGTGCAGAAACTTCAATTCATGGC
ATAAATTTTATTCTTACTTGCAATCAAAATTGGATAAATAGAATTTTTTGGTTCTTAGCT
CTTGTCATTTCTTCAATTTTGCTTGCATTAAATGTAAATTTAGCTTATCAAAAATATCAA
AATGAGCCATCAATTGTCATTAGGAGTAACATGAGAGATTTAAAAGAAATTCCAATGCCT
GCTTTAACAATTTGCTCACCATTATTTGCTATAAATAATTTGGCAAATTTGAATAATTTT
TACAAAAATTATTATGAGAAAAAAATTTTTGCTGCAAATATGACATCAAAAGAAGCGAAT
TATTTAATGGCAAATTTACAAGTCTGCAGACCAAATTCAATTTTTGACCTTGCAAAATTT
ATTTCAAATAGAACTGACACAAATATTGTAAAATTATTGCTTGAAAGTTCTCAAAGTGTT
GAAGAATTTTTGGTTAAATGTTTTTTAAAATATTTTCCTAAAAATTGCACAAAAATGATG
AACAGAATTTTAACTGACAAAGGTTTTTGTTATACATTTAATATGCAAGATTTTGATATC
ATTTTTAATGCTGAAAAAATCAGTGAAGATTTTTATTCTTATAAAAAAGAGAAAATAATT
ATGTCCAATAATTCCTCTAATGATAAGAAAGTTCATCTTCAATGGACACTTGAAAAAGGT
TTCAGTCCAAATCACAAAGACGATGACATTCCAATTCCTGCATTTATGAGAAAAGAAAGT
GGAATAATTATGCGATTAGATGAAAAAGACTCAAAAAATGTTTGTCATGAAAATTTAGTT
CTTACTTATTTTCTACATTTACCAAATGAAATTCCAACACCATTTCATCATACAAACATT
ATAAAATTTAATGACACAGAGACAATCACTTTGACAGCAAAAATGTATAAGACAAATGAA
AATCTTCGTGGTTATTCACCTGAAATTCGTAGTTGTTATTTTGAGGGTGAAAAAAAATTG
AAATTTTTCAAGTCTTACACAAAAGCAAATTGTGAATTTGAATGCATGGCAAATCAAACT
TTTGAAACTTGTGGATGTGTGAAATTTTCAATGCCAAGGGAGAATCACACAAAAGTTTGT
GATGAGACAAAAATCAAATGTGTTTTGAACGTTATGATGAATTTTCCAAATAGTAATGGA
AATTTTGAATCTTGTGACTGCTTAAAACCTTGCAGTGATATAAAATATTTTGTGGCATTC
AGAGATGCTTCATTATTTTCATATCAACATGGTTTTAATAGAAGTGCAATGTCTGTGTTT
TCTTTTCGATTTGATGATTTTTCAATTGAAGAAGAGGAAAAATATTCAGCCTATACATTT
CAAATTTATGCGGATCGTCAGAAATTTCAAGCATGGAAGCAAAAACATCAAAAAGTTTAC
AAATCTCCGACAGATGAAGATCAAGCAATGGAAAATATGCTAAGAAATCAAAAAGAAATT
GACGAACATAACAAACTTTTTGAACAAGGTAAAGTGACTTTTACAAGAGCAACATGGGAA
CATTCTGACCTTGATTATGAACAGAAGTTGAAGAAATTGACTGGCAATAAAGGTCAAGCA
TCGAATGATTCAATTATGATGTCAAGTTTTGTACAAGCTTCGAAATCAAACATTCAAAAA
AGTCCAGATGAAGTTGACTGGGTAAAATCTGGATTAGTTAATTCAATTAGAAATCAAGGA
AAGTGTGGAAGTTGCTGGGCTTTTACAGCTGTTGGAGTAGCTGATGGTGCTCTTCTAAAA
CAAGGAATAAAAACAAGGCTTTCAGAACAAAACCTTGTCGATTGCAGTAAAGCTAATTAT
GGCTGTGATGGTGGAGATGCTTATTCAGGACTAAAATTTATTGCATCCAAAGGAATTTCA
TCAATTTCCGATTATCCATACACTGGGAAAGATGGAAAATGCAAAAATTTGAAGAAAGTA
AATTTCAATCTTGGAAATATAAAATATGAAAAATTACGAGGAAATGAAAATCGATTGAAA
GATATTGTTGCTAATTTTGGACCGGTTGGTGTTGCAATTGATGCTGCTGATTCATTTATG
AATTATGAATCAGGAGTTTACAATAATCCAAAATGTTCTAAAAGAGCTAATCATGCTGTG
CTTTTGGTTGGTTATGGAAGAGATGAAAAATTAAATATGGATTATTGGTTGGTTAAAAAT
TCTTGGGGAACATCGTGGGGTGAAAATGGTTACGTTAGAATGGCAAGGAATAAAAATAAT
CAATGTGCAATAGCTGGAGAAGTTACTTACATTTTATGA
>g16342.t1 Gene=g16342 Length=772
MFQTVLEIFSTFGAETSIHGINFILTCNQNWINRIFWFLALVISSILLALNVNLAYQKYQ
NEPSIVIRSNMRDLKEIPMPALTICSPLFAINNLANLNNFYKNYYEKKIFAANMTSKEAN
YLMANLQVCRPNSIFDLAKFISNRTDTNIVKLLLESSQSVEEFLVKCFLKYFPKNCTKMM
NRILTDKGFCYTFNMQDFDIIFNAEKISEDFYSYKKEKIIMSNNSSNDKKVHLQWTLEKG
FSPNHKDDDIPIPAFMRKESGIIMRLDEKDSKNVCHENLVLTYFLHLPNEIPTPFHHTNI
IKFNDTETITLTAKMYKTNENLRGYSPEIRSCYFEGEKKLKFFKSYTKANCEFECMANQT
FETCGCVKFSMPRENHTKVCDETKIKCVLNVMMNFPNSNGNFESCDCLKPCSDIKYFVAF
RDASLFSYQHGFNRSAMSVFSFRFDDFSIEEEEKYSAYTFQIYADRQKFQAWKQKHQKVY
KSPTDEDQAMENMLRNQKEIDEHNKLFEQGKVTFTRATWEHSDLDYEQKLKKLTGNKGQA
SNDSIMMSSFVQASKSNIQKSPDEVDWVKSGLVNSIRNQGKCGSCWAFTAVGVADGALLK
QGIKTRLSEQNLVDCSKANYGCDGGDAYSGLKFIASKGISSISDYPYTGKDGKCKNLKKV
NFNLGNIKYEKLRGNENRLKDIVANFGPVGVAIDAADSFMNYESGVYNNPKCSKRANHAV
LLVGYGRDEKLNMDYWLVKNSWGTSWGENGYVRMARNKNNQCAIAGEVTYIL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g16342.t1 | CDD | cd02248 | Peptidase_C1A | 562 | 771 | 4.23554E-90 |
| 14 | g16342.t1 | Gene3D | G3DSA:1.10.287.770 | - | 34 | 63 | 1.6E-12 |
| 11 | g16342.t1 | Gene3D | G3DSA:2.60.470.10 | - | 64 | 196 | 1.6E-12 |
| 12 | g16342.t1 | Gene3D | G3DSA:1.10.3590.10 | - | 88 | 158 | 1.6E-12 |
| 13 | g16342.t1 | Gene3D | G3DSA:1.10.287.820 | - | 329 | 411 | 2.1E-9 |
| 10 | g16342.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 461 | 772 | 6.3E-89 |
| 4 | g16342.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 464 | 768 | 1.5E-69 |
| 5 | g16342.t1 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 464 | 768 | 1.5E-69 |
| 8 | g16342.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 579 | 594 | 6.0E-9 |
| 6 | g16342.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 718 | 728 | 6.0E-9 |
| 7 | g16342.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 735 | 741 | 6.0E-9 |
| 2 | g16342.t1 | Pfam | PF00858 | Amiloride-sensitive sodium channel | 12 | 475 | 2.6E-48 |
| 1 | g16342.t1 | Pfam | PF08246 | Cathepsin propeptide inhibitor domain (I29) | 469 | 527 | 5.8E-6 |
| 3 | g16342.t1 | Pfam | PF00112 | Papain family cysteine protease | 562 | 770 | 1.8E-68 |
| 16 | g16342.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 34 | - |
| 18 | g16342.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 56 | - |
| 15 | g16342.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 57 | 76 | - |
| 19 | g16342.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 77 | 95 | - |
| 17 | g16342.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 96 | 772 | - |
| 24 | g16342.t1 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 579 | 590 | - |
| 23 | g16342.t1 | ProSitePatterns | PS00639 | Eukaryotic thiol (cysteine) proteases histidine active site. | 716 | 726 | - |
| 22 | g16342.t1 | ProSitePatterns | PS00640 | Eukaryotic thiol (cysteine) proteases asparagine active site. | 735 | 754 | - |
| 26 | g16342.t1 | SMART | SM00848 | Inhibitor_I29_2 | 469 | 529 | 7.5E-8 |
| 25 | g16342.t1 | SMART | SM00645 | pept_c1 | 561 | 772 | 6.7E-82 |
| 9 | g16342.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 467 | 770 | 2.0E-88 |
| 21 | g16342.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 57 | - |
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:0016020 | membrane | CC |
| GO:0008234 | cysteine-type peptidase activity | MF |
| GO:0006508 | proteolysis | BP |
| GO:0005272 | sodium channel activity | MF |
| GO:0006814 | sodium ion transport | 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