General information for g1247.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Lysozyme c-1.
Parent gene
- The parent gene g1247 is located on chr_3: 9119015..9120245 (+ 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 | g1247 | g1247.t1 | TSS | g1247.t1 | 9118955 | 9118955 |
| chr_3 | g1247 | g1247.t1 | isoform | g1247.t1 | 9119015 | 9120245 |
| chr_3 | g1247 | g1247.t1 | exon | g1247.t1.exon1 | 9119015 | 9119300 |
| chr_3 | g1247 | g1247.t1 | cds | g1247.t1.CDS1 | 9119015 | 9119300 |
| chr_3 | g1247 | g1247.t1 | exon | g1247.t1.exon2 | 9119358 | 9119486 |
| chr_3 | g1247 | g1247.t1 | cds | g1247.t1.CDS2 | 9119358 | 9119486 |
| chr_3 | g1247 | g1247.t1 | exon | g1247.t1.exon3 | 9120022 | 9120245 |
| chr_3 | g1247 | g1247.t1 | cds | g1247.t1.CDS3 | 9120022 | 9120245 |
| chr_3 | g1247 | g1247.t1 | TTS | g1247.t1 | NA | NA |
Sequences
>g1247.t1 Gene=g1247 Length=639
ATGAAATTTTTAATTGCTGCAATTTTATTTGTTGCAATTTTTGCTAATATTAACGCAAAA
ATTTATTCAAAATGTGAGCTCGTTCGAACACTTTATAATTCTGGTATTCCACAAAGTCAG
TTACGTGATTGGGCATGCTTAGTACAACATGAAAGTAGCTACAACTCAAAAGCAAAAGGA
GGACCAAACAAAAATGGCTCATATGACTATGGAATTTTTCAAATCAATTCAAAATATTGG
TGTGGAATTGGAAAAGTTGGTGGAGATTGTAATTTAAATTGCAATTCTTTGCTTACTGAT
GATATTAGTGATGACATTCGATGTGCAAAGATAATCTATAAACGTCATAATTTCAGTGCT
TGGTATGGTTGGGTTAATCATTGCAAAGGAAAAGCTCTGCCATCAATTTCAGAATATGCA
AGAGTTTTTACAAATTGCCAATTTGTTCAAGCTCTTTCACGAGTTAGAATTCCTAAAGGT
GATTTACCAACATGGGCTTGTATTGCACAACATGAGAGCAATTATAACACATCTGCAGTC
AACAACTTTAATACTGATGGATCAAAAGACTTTGGAATTTTTCAAATCAACTCAAGATAT
TGGTTAAAATTGGATCTGTTGGAAACGACTGCAACTTGA
>g1247.t1 Gene=g1247 Length=212
MKFLIAAILFVAIFANINAKIYSKCELVRTLYNSGIPQSQLRDWACLVQHESSYNSKAKG
GPNKNGSYDYGIFQINSKYWCGIGKVGGDCNLNCNSLLTDDISDDIRCAKIIYKRHNFSA
WYGWVNHCKGKALPSISEYARVFTNCQFVQALSRVRIPKGDLPTWACIAQHESNYNTSAV
NNFNTDGSKDFGIFQINSRYWLKLDLLETTAT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 28 | g1247.t1 | CDD | cd16899 | LYZ_C_invert | 20 | 138 | 7.60668E-67 |
| 21 | g1247.t1 | Gene3D | G3DSA:1.10.530.10 | - | 20 | 86 | 8.1E-27 |
| 22 | g1247.t1 | Gene3D | G3DSA:1.10.530.10 | - | 88 | 141 | 2.0E-17 |
| 20 | g1247.t1 | Gene3D | G3DSA:1.10.530.10 | - | 142 | 205 | 7.7E-23 |
| 3 | g1247.t1 | PANTHER | PTHR11407 | LYSOZYME C | 1 | 138 | 9.8E-76 |
| 5 | g1247.t1 | PANTHER | PTHR11407:SF36 | GEO02684P1-RELATED | 1 | 138 | 9.8E-76 |
| 4 | g1247.t1 | PANTHER | PTHR11407 | LYSOZYME C | 139 | 203 | 9.8E-76 |
| 6 | g1247.t1 | PANTHER | PTHR11407:SF36 | GEO02684P1-RELATED | 139 | 203 | 9.8E-76 |
| 16 | g1247.t1 | PRINTS | PR00137 | Lysozyme signature | 21 | 39 | 3.0E-8 |
| 10 | g1247.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 22 | 32 | 1.7E-19 |
| 9 | g1247.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 39 | 48 | 1.7E-19 |
| 11 | g1247.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 67 | 83 | 1.7E-19 |
| 8 | g1247.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 88 | 97 | 1.7E-19 |
| 13 | g1247.t1 | PRINTS | PR00137 | Lysozyme signature | 95 | 110 | 3.0E-8 |
| 7 | g1247.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 98 | 113 | 1.7E-19 |
| 14 | g1247.t1 | PRINTS | PR00137 | Lysozyme signature | 116 | 125 | 3.0E-8 |
| 12 | g1247.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 117 | 128 | 1.7E-19 |
| 15 | g1247.t1 | PRINTS | PR00137 | Lysozyme signature | 126 | 139 | 3.0E-8 |
| 2 | g1247.t1 | Pfam | PF00062 | C-type lysozyme/alpha-lactalbumin family | 20 | 135 | 2.2E-31 |
| 1 | g1247.t1 | Pfam | PF00062 | C-type lysozyme/alpha-lactalbumin family | 141 | 203 | 1.3E-14 |
| 24 | g1247.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 25 | g1247.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 26 | g1247.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 27 | g1247.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 23 | g1247.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 212 | - |
| 31 | g1247.t1 | ProSitePatterns | PS00128 | Glycosyl hydrolases family 22 (GH22) domain signature. | 90 | 108 | - |
| 33 | g1247.t1 | ProSiteProfiles | PS51348 | Glycosyl hydrolases family 22 (GH22) domain profile. | 20 | 149 | 36.663 |
| 32 | g1247.t1 | ProSiteProfiles | PS51348 | Glycosyl hydrolases family 22 (GH22) domain profile. | 141 | 212 | 19.854 |
| 29 | g1247.t1 | SMART | SM00263 | lysozyme-fin | 20 | 140 | 4.4E-51 |
| 30 | g1247.t1 | SMART | SM00263 | lysozyme-fin | 141 | 210 | 7.8E-6 |
| 18 | g1247.t1 | SUPERFAMILY | SSF53955 | Lysozyme-like | 19 | 136 | 5.36E-45 |
| 17 | g1247.t1 | SUPERFAMILY | SSF53955 | Lysozyme-like | 141 | 203 | 1.26E-22 |
| 19 | g1247.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
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:0003796 | lysozyme activity | MF |
KEGG
Orthology
- This transcript has been annotated with K13915 (lysozyme C)
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