General information for g488.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Modular serine protease.
Parent gene
- The parent gene g488 is located on chr_3: 3688630..3691632 (+ 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_3 | g488 | g488.t1 | isoform | g488.t1 | 3688630 | 3691632 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon1 | 3688630 | 3688681 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS1 | 3688630 | 3688681 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon2 | 3688751 | 3689051 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS2 | 3688751 | 3689051 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon3 | 3689170 | 3689672 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS3 | 3689170 | 3689672 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon4 | 3689890 | 3690188 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS4 | 3689890 | 3690188 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon5 | 3690377 | 3690461 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS5 | 3690377 | 3690461 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon6 | 3690518 | 3690700 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS6 | 3690518 | 3690700 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon7 | 3690761 | 3690898 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS7 | 3690761 | 3690898 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon8 | 3691048 | 3691227 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS8 | 3691048 | 3691227 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon9 | 3691285 | 3691299 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS9 | 3691285 | 3691299 |
| chr_3 | g488 | g488.t1 | exon | g488.t1.exon10 | 3691457 | 3691632 |
| chr_3 | g488 | g488.t1 | cds | g488.t1.CDS10 | 3691457 | 3691632 |
| chr_3 | g488 | g488.t1 | TSS | g488.t1 | NA | NA |
| chr_3 | g488 | g488.t1 | TTS | g488.t1 | NA | NA |
Sequences
>g488.t1 Gene=g488 Length=1932
ATGAAATTAAATAAAAATTTCCTAATTTTCATCACAATTTGTCAAATATTTCTAACTCTC
AAAGTTCTCACATCACCAACATGTGGACCATTTGAATATAAATGCACAACTGATGGCTCA
TGCATTTCAGAAGAATTAGTTTGTGATGGCAAAAGTGATTGCCCAAATAGAACTGATGAA
ATGGAAGAACTTTGCACAAGAGTCAGTTGTCCTAGATACAGTTTTAGATGTGCTTATGGT
GCATGCATAGATCAATGGAAAGTTTGTAATGGCAAGAAAGATTGCCTTGATGGTTCTGAT
GAATTAATTATAAATTGCAAGGAAGAAGAAGAAAATGAACTTGTTGGTTGTCCCATTGAC
AAGTACAGATGTCGTTCAGGTGACTGCATAAATTCTGATTTAGTCTGCAATGGAGCAGTT
GATTGTCCTGATGGTTCTGATGAAGAAGAAAACATTTGCCTCAAGTCATTTTGCCCTAAA
AAAGCCTTTCGCTGTCGCTATGGAGCTTGCGTTCCCAAATATGTTCGTTGTAGTGGAGTT
TCATATTGCGCTGATGGATCAGATGAAGATGAACTTTTATGTGGAGCAAATTACGATGGT
TACGTATTAAAAGGGAATGTTTCAGGAAAAATTCCACCAGGAAGTTGTCGTTTGCCAACA
AGAGATGATATAAGATATATGAATTATATTTTCGGTGAAGAATACTTGCCTGGTGCTTAT
GTCAATGATGGAGAATATATTGAAGTTCTTTGTAATCGTGGAACTGCTATGAATGTTTCT
ACTAACTTTGATCTATCTAATACTTGCAATAATACGAAATGGACGAGGAAATGGAATGTT
TTTCCTGAATGTCAAACAATTTGCAGTGGAGCAGACGTAATAGGACGAACGATAAAAACA
ATGTGTGAATTGAATGGTGAAATTGTTCCATGCAATCAGCAACATTTAGTCGGAACAATA
GCTTACATCACATGTGGTTCATATTATGAAATGCCAACAGGCGTTGATACTTCACATTTA
TCACAGAAATTGACATGCTTGTCGAGTGGAAGTTGGGATAAAGTTGCACTTAGATGTACA
CCAAGATGTGGACGAGTTACTCAAGCATCACAAGCTTATGTTGTGAATGGTAGGAAGGCA
AAAAATATTGCTGAAGTCCCTTGGAGTGCAGCAATATACAAGCGTGACATTTTAATATGT
GGTGGGACAATAATTTCTGAAAAACTCATCATTTCTGCAGCTCATTGCTTTTTCAGAGAA
CAACCAAGCAGTCTTTCAGAAGCAGTTGTGCTAGAAGACCTTTCACTTTTCAAGGTTGCA
GTTGGAAAATATTTTCGTGATATGAATGCTCAAGAGACTTTTCAGCCACAATTCTTCAAT
GTTAGTGAAGTCATATCGGTTCCTGGGTATGACGGCTATATGGGTTTCTTTGCTGCTGAT
TTCATAATTATTGTTCTTGATGATTTTATAATATTTAGACAACATATTGTTCCAATTTGT
GTTGATAAAAATGCAGATTTAGAAGAAGATATGATTGTTCCTGAAGGATTAACTGGAACT
GTTGCTGGCTATGGCTTCACAACAGCTGGTGGAAGTCCAAGTGACGTCCTGAAAATTGCA
AAACTTCCAACTGTCAGCTACAGTCAATGCAAAAAAGAAGCACCACAAAATTTCAAACAA
TTTGTTACACCTGATAAATTTTGTGCTGGAAATACTCATGGTGGTGATGCTGTTTGTCAA
GGTGATTCTGGATCAGGTTTAGTTTTCCCACAAATGATAAAAGATGAAGAAGTTTATTTC
CTTCGTGGATTAGTCAGCAATGCACGACAAGTCGAAGGAGAATGTGATTTAAGCTTTTAT
ACAATGTTTACAAACATTCATCAATATGTTCGTTTTATTAAATCAGCTTATAAAAAATAT
CCTTCGTCTTAA
>g488.t1 Gene=g488 Length=643
MKLNKNFLIFITICQIFLTLKVLTSPTCGPFEYKCTTDGSCISEELVCDGKSDCPNRTDE
MEELCTRVSCPRYSFRCAYGACIDQWKVCNGKKDCLDGSDELIINCKEEEENELVGCPID
KYRCRSGDCINSDLVCNGAVDCPDGSDEEENICLKSFCPKKAFRCRYGACVPKYVRCSGV
SYCADGSDEDELLCGANYDGYVLKGNVSGKIPPGSCRLPTRDDIRYMNYIFGEEYLPGAY
VNDGEYIEVLCNRGTAMNVSTNFDLSNTCNNTKWTRKWNVFPECQTICSGADVIGRTIKT
MCELNGEIVPCNQQHLVGTIAYITCGSYYEMPTGVDTSHLSQKLTCLSSGSWDKVALRCT
PRCGRVTQASQAYVVNGRKAKNIAEVPWSAAIYKRDILICGGTIISEKLIISAAHCFFRE
QPSSLSEAVVLEDLSLFKVAVGKYFRDMNAQETFQPQFFNVSEVISVPGYDGYMGFFAAD
FIIIVLDDFIIFRQHIVPICVDKNADLEEDMIVPEGLTGTVAGYGFTTAGGSPSDVLKIA
KLPTVSYSQCKKEAPQNFKQFVTPDKFCAGNTHGGDAVCQGDSGSGLVFPQMIKDEEVYF
LRGLVSNARQVEGECDLSFYTMFTNIHQYVRFIKSAYKKYPSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 32 | g488.t1 | CDD | cd00112 | LDLa | 28 | 61 | 2.36116E-6 |
| 30 | g488.t1 | CDD | cd00112 | LDLa | 70 | 106 | 2.22698E-9 |
| 29 | g488.t1 | CDD | cd00112 | LDLa | 117 | 149 | 8.51246E-9 |
| 31 | g488.t1 | CDD | cd00112 | LDLa | 158 | 190 | 5.57757E-5 |
| 33 | g488.t1 | CDD | cd00190 | Tryp_SPc | 374 | 635 | 1.15207E-38 |
| 22 | g488.t1 | Gene3D | G3DSA:4.10.400.10 | - | 26 | 73 | 2.5E-10 |
| 19 | g488.t1 | Gene3D | G3DSA:4.10.400.10 | - | 74 | 101 | 7.2E-11 |
| 21 | g488.t1 | Gene3D | G3DSA:4.10.400.10 | - | 115 | 155 | 7.8E-11 |
| 20 | g488.t1 | Gene3D | G3DSA:4.10.400.10 | - | 156 | 196 | 3.7E-9 |
| 18 | g488.t1 | Gene3D | G3DSA:2.10.70.10 | Complement Module | 302 | 361 | 8.1E-5 |
| 23 | g488.t1 | Gene3D | G3DSA:2.40.10.10 | - | 366 | 638 | 3.0E-47 |
| 6 | g488.t1 | PANTHER | PTHR24260 | - | 13 | 640 | 2.5E-66 |
| 7 | g488.t1 | PANTHER | PTHR24260:SF129 | MODULAR SERINE PROTEASE | 13 | 640 | 2.5E-66 |
| 11 | g488.t1 | PRINTS | PR00261 | Low density lipoprotein (LDL) receptor signature | 39 | 60 | 8.6E-23 |
| 10 | g488.t1 | PRINTS | PR00261 | Low density lipoprotein (LDL) receptor signature | 80 | 101 | 8.6E-23 |
| 9 | g488.t1 | PRINTS | PR00261 | Low density lipoprotein (LDL) receptor signature | 127 | 148 | 8.6E-23 |
| 8 | g488.t1 | PRINTS | PR00261 | Low density lipoprotein (LDL) receptor signature | 168 | 189 | 8.6E-23 |
| 2 | g488.t1 | Pfam | PF00057 | Low-density lipoprotein receptor domain class A | 27 | 63 | 1.6E-7 |
| 3 | g488.t1 | Pfam | PF00057 | Low-density lipoprotein receptor domain class A | 69 | 106 | 4.1E-10 |
| 5 | g488.t1 | Pfam | PF00057 | Low-density lipoprotein receptor domain class A | 117 | 150 | 6.6E-10 |
| 4 | g488.t1 | Pfam | PF00057 | Low-density lipoprotein receptor domain class A | 158 | 190 | 4.5E-7 |
| 1 | g488.t1 | Pfam | PF00089 | Trypsin | 375 | 633 | 7.1E-31 |
| 25 | g488.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 24 | - |
| 26 | g488.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 27 | g488.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 20 | - |
| 28 | g488.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 24 | - |
| 24 | g488.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 25 | 643 | - |
| 39 | g488.t1 | ProSitePatterns | PS01209 | LDL-receptor class A (LDLRA) domain signature. | 129 | 153 | - |
| 40 | g488.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 411 | 416 | - |
| 44 | g488.t1 | ProSiteProfiles | PS50068 | LDL-receptor class A (LDLRA) domain profile. | 27 | 66 | 11.963 |
| 43 | g488.t1 | ProSiteProfiles | PS50068 | LDL-receptor class A (LDLRA) domain profile. | 69 | 107 | 12.238 |
| 42 | g488.t1 | ProSiteProfiles | PS50068 | LDL-receptor class A (LDLRA) domain profile. | 116 | 154 | 11.975 |
| 45 | g488.t1 | ProSiteProfiles | PS50068 | LDL-receptor class A (LDLRA) domain profile. | 157 | 195 | 10.8 |
| 41 | g488.t1 | ProSiteProfiles | PS50240 | Serine proteases, trypsin domain profile. | 374 | 638 | 23.248 |
| 37 | g488.t1 | SMART | SM00192 | LDLa_2 | 27 | 67 | 1.5E-9 |
| 35 | g488.t1 | SMART | SM00192 | LDLa_2 | 69 | 108 | 2.9E-12 |
| 36 | g488.t1 | SMART | SM00192 | LDLa_2 | 116 | 155 | 3.4E-9 |
| 38 | g488.t1 | SMART | SM00192 | LDLa_2 | 157 | 196 | 4.5E-6 |
| 34 | g488.t1 | SMART | SM00020 | trypsin_2 | 373 | 633 | 2.2E-29 |
| 12 | g488.t1 | SUPERFAMILY | SSF57424 | LDL receptor-like module | 26 | 65 | 4.32E-8 |
| 14 | g488.t1 | SUPERFAMILY | SSF57424 | LDL receptor-like module | 64 | 102 | 3.8E-10 |
| 15 | g488.t1 | SUPERFAMILY | SSF57424 | LDL receptor-like module | 114 | 153 | 2.36E-9 |
| 13 | g488.t1 | SUPERFAMILY | SSF57424 | LDL receptor-like module | 150 | 193 | 1.27E-8 |
| 16 | g488.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 343 | 636 | 7.01E-53 |
| 17 | g488.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
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 |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K20674 (modular serine protease [EC:3.4.21.-])
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. There were no conditions that were differentially expressed