General information for g16944.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cathepsin L1.
Parent gene
- The parent gene g16944 is located on chr_4: 11835962..11837787 (- 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 | g16944 | g16944.t1 | isoform | g16944.t1 | 11835962 | 11837787 |
| chr_4 | g16944 | g16944.t1 | exon | g16944.t1.exon1 | 11835962 | 11836034 |
| chr_4 | g16944 | g16944.t1 | cds | g16944.t1.CDS1 | 11835962 | 11836034 |
| chr_4 | g16944 | g16944.t1 | exon | g16944.t1.exon2 | 11836326 | 11836347 |
| chr_4 | g16944 | g16944.t1 | cds | g16944.t1.CDS2 | 11836326 | 11836347 |
| chr_4 | g16944 | g16944.t1 | exon | g16944.t1.exon3 | 11836406 | 11836785 |
| chr_4 | g16944 | g16944.t1 | cds | g16944.t1.CDS3 | 11836406 | 11836785 |
| chr_4 | g16944 | g16944.t1 | exon | g16944.t1.exon4 | 11836841 | 11836933 |
| chr_4 | g16944 | g16944.t1 | cds | g16944.t1.CDS4 | 11836841 | 11836933 |
| chr_4 | g16944 | g16944.t1 | exon | g16944.t1.exon5 | 11836986 | 11837014 |
| chr_4 | g16944 | g16944.t1 | cds | g16944.t1.CDS5 | 11836986 | 11837014 |
| chr_4 | g16944 | g16944.t1 | exon | g16944.t1.exon6 | 11837305 | 11837787 |
| chr_4 | g16944 | g16944.t1 | cds | g16944.t1.CDS6 | 11837305 | 11837787 |
| chr_4 | g16944 | g16944.t1 | TSS | g16944.t1 | NA | NA |
| chr_4 | g16944 | g16944.t1 | TTS | g16944.t1 | NA | NA |
Sequences
>g16944.t1 Gene=g16944 Length=1080
ATGAAAATAACATTAGTGTTTTTTGGATTTCTTGCCATAAATTTGGCATCATCATCGAAA
ATTTTTAAAATTGCGATTGATTTAGAAAGTGGAAAAGAACAAAATGTTGAAGTTGTAGAA
CTTGATCAACCACAAGAAATTGTCGATGAACAAGAAGAAATTGAAACTGATTCATTCAAT
ATTTTTCTCAAAACTTTCAACATCCAACTTGAAAACTACGAAATGCGTCAAAAAATATTT
ACTAAAAACTACAGAAAAATTCGACATCACAATGAACGCTTTTATAAAGGACTTGAAACA
TTTGAAATGGCTGTAAATAAATTTACTCATTTGACTGAAATTGAAAGAAAGAATTTTATT
AGTCAAATTCATCCAAGAGAAGCTACAAATTTTTCAATTCCTATTTATAAAGTTAAATTT
GATGATAGCGAATTAGCTTCAAGTGTCAATTGGGTTGAGAAAAACAAACTTCAACCAATT
CAGGACCAAGGACAATGTGAAAGTTGCTATGCTTTTGCTGCAATTGCAACAATTGAATCA
CAAATGATAATTCGTTACAATAATTGGGAAAAACTTTCAGAACAAGAAGCAATGGAGTGC
ACAAAAGGTTGCAAAGGTGGACTATCACAAGATATTTATTTGTATTCACAAGTTCATGGT
GGTTGTGCATCTGAAAATTCTTATCCTTATTACGGTCATGAAGTTAATGACTGCAATGCA
GCTCAAAACCGTAAACGTGTTTCTAACAGTAAATGCACTGGAATTTTAGAATTTGGAACT
TCCGTGGAAGCAACTATGAAAGCAATCGAACAATTTGGACCAATAACTGCTTATATGGCA
ATTTACAATAGTTTCTATAATTACAATAATGGAATCTACAAAAGAACCCAAAATGATGAT
GAAATTCAAGGATATCATGCTGTAACTTTTGTTGGTTATGGACAAGAAAATGGCCTAGAT
TATTGGCTTGTTAGAAATTCTTGGGGCAAACATTGGGGACAAAATGGATATGCTAAATTC
CTCAAAGGCACAGATGAATGTGAAATTGAATCTTTAAATCATTATGGACCACAATTGTAA
>g16944.t1 Gene=g16944 Length=359
MKITLVFFGFLAINLASSSKIFKIAIDLESGKEQNVEVVELDQPQEIVDEQEEIETDSFN
IFLKTFNIQLENYEMRQKIFTKNYRKIRHHNERFYKGLETFEMAVNKFTHLTEIERKNFI
SQIHPREATNFSIPIYKVKFDDSELASSVNWVEKNKLQPIQDQGQCESCYAFAAIATIES
QMIIRYNNWEKLSEQEAMECTKGCKGGLSQDIYLYSQVHGGCASENSYPYYGHEVNDCNA
AQNRKRVSNSKCTGILEFGTSVEATMKAIEQFGPITAYMAIYNSFYNYNNGIYKRTQNDD
EIQGYHAVTFVGYGQENGLDYWLVRNSWGKHWGQNGYAKFLKGTDECEIESLNHYGPQL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g16944.t1 | CDD | cd02248 | Peptidase_C1A | 148 | 351 | 8.93868E-62 |
| 9 | g16944.t1 | Gene3D | G3DSA:3.90.70.10 | Cysteine proteinases | 50 | 356 | 8.1E-74 |
| 2 | g16944.t1 | PANTHER | PTHR12411 | CYSTEINE PROTEASE FAMILY C1-RELATED | 63 | 351 | 5.1E-51 |
| 3 | g16944.t1 | PANTHER | PTHR12411:SF57 | CATHEPSIN L1 | 63 | 351 | 5.1E-51 |
| 5 | g16944.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 163 | 178 | 1.9E-7 |
| 6 | g16944.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 306 | 316 | 1.9E-7 |
| 4 | g16944.t1 | PRINTS | PR00705 | Papain cysteine protease (C1) family signature | 321 | 327 | 1.9E-7 |
| 1 | g16944.t1 | Pfam | PF00112 | Papain family cysteine protease | 146 | 355 | 1.1E-54 |
| 11 | g16944.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 12 | g16944.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 13 | g16944.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 14 | g16944.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 10 | g16944.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 359 | - |
| 16 | g16944.t1 | ProSitePatterns | PS00139 | Eukaryotic thiol (cysteine) proteases cysteine active site. | 163 | 174 | - |
| 18 | g16944.t1 | SMART | SM00848 | Inhibitor_I29_2 | 59 | 116 | 4.8E-7 |
| 17 | g16944.t1 | SMART | SM00645 | pept_c1 | 145 | 357 | 1.3E-47 |
| 7 | g16944.t1 | SUPERFAMILY | SSF54001 | Cysteine proteinases | 57 | 355 | 3.39E-74 |
| 8 | g16944.t1 | SignalP_EUK | 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:0008234 | cysteine-type peptidase 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.
