General information for g1245.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 g1245 is located on chr_3: 9116757..9117245 (+ 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 | g1245 | g1245.t1 | isoform | g1245.t1 | 9116757 | 9117245 |
| chr_3 | g1245 | g1245.t1 | exon | g1245.t1.exon1 | 9116757 | 9117042 |
| chr_3 | g1245 | g1245.t1 | cds | g1245.t1.CDS1 | 9116757 | 9117042 |
| chr_3 | g1245 | g1245.t1 | exon | g1245.t1.exon2 | 9117106 | 9117245 |
| chr_3 | g1245 | g1245.t1 | cds | g1245.t1.CDS2 | 9117106 | 9117245 |
| chr_3 | g1245 | g1245.t1 | TTS | g1245.t1 | 9117375 | 9117375 |
| chr_3 | g1245 | g1245.t1 | TSS | g1245.t1 | NA | NA |
Sequences
>g1245.t1 Gene=g1245 Length=426
ATGAAACTTATAATTTTTATTACAATTTTAATTGCAACTTTTACATTTTCTGAAGCAAAA
GTTTTCTCAAAATGTGAATTTGTTAAAACTCTTTACAATGCTGGAGTCCCGAGAAACGAA
TTACGTGATTGGGCTTGCATCGCTCAATATGAAAGTAACTATAACACAGCTGCTATCAAT
AATTACAACACTGATGGATCAAAAGATTTTGGAATTTTTCAAATCAACTCAAGATATTGG
TGCAAAATTGGATCTGTTGGAAATGACTGCAACTTGAACTGCAATTCTTTGCTCAATGAT
AATATTAGTGATGATATTAAATGTGCTAGATTGATTAAAAGCAGACAAGGATTTTCGGCT
TGGGTAGCATGGAACAATCGATGCCAAGGAAAAACTCTTCCTACTGTTTCAGAATGTGGT
TTTTAA
>g1245.t1 Gene=g1245 Length=141
MKLIIFITILIATFTFSEAKVFSKCEFVKTLYNAGVPRNELRDWACIAQYESNYNTAAIN
NYNTDGSKDFGIFQINSRYWCKIGSVGNDCNLNCNSLLNDNISDDIKCARLIKSRQGFSA
WVAWNNRCQGKTLPTVSECGF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g1245.t1 | CDD | cd16899 | LYZ_C_invert | 20 | 139 | 2.19867E-65 |
| 17 | g1245.t1 | Gene3D | G3DSA:1.10.530.10 | - | 20 | 86 | 5.1E-28 |
| 18 | g1245.t1 | Gene3D | G3DSA:1.10.530.10 | - | 87 | 141 | 2.2E-18 |
| 2 | g1245.t1 | PANTHER | PTHR11407 | LYSOZYME C | 1 | 139 | 1.6E-53 |
| 3 | g1245.t1 | PANTHER | PTHR11407:SF36 | GEO02684P1-RELATED | 1 | 139 | 1.6E-53 |
| 13 | g1245.t1 | PRINTS | PR00137 | Lysozyme signature | 21 | 39 | 6.6E-10 |
| 7 | g1245.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 22 | 32 | 9.0E-21 |
| 6 | g1245.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 39 | 48 | 9.0E-21 |
| 8 | g1245.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 67 | 83 | 9.0E-21 |
| 11 | g1245.t1 | PRINTS | PR00137 | Lysozyme signature | 84 | 94 | 6.6E-10 |
| 5 | g1245.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 88 | 97 | 9.0E-21 |
| 10 | g1245.t1 | PRINTS | PR00137 | Lysozyme signature | 95 | 110 | 6.6E-10 |
| 4 | g1245.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 98 | 113 | 9.0E-21 |
| 12 | g1245.t1 | PRINTS | PR00137 | Lysozyme signature | 116 | 125 | 6.6E-10 |
| 9 | g1245.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 117 | 128 | 9.0E-21 |
| 1 | g1245.t1 | Pfam | PF00062 | C-type lysozyme/alpha-lactalbumin family | 20 | 139 | 1.1E-34 |
| 20 | g1245.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 21 | g1245.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 22 | g1245.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 23 | g1245.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 19 | g1245.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 141 | - |
| 26 | g1245.t1 | ProSitePatterns | PS00128 | Glycosyl hydrolases family 22 (GH22) domain signature. | 90 | 108 | - |
| 27 | g1245.t1 | ProSiteProfiles | PS51348 | Glycosyl hydrolases family 22 (GH22) domain profile. | 20 | 141 | 38.328 |
| 25 | g1245.t1 | SMART | SM00263 | lysozyme-fin | 20 | 140 | 7.3E-56 |
| 14 | g1245.t1 | SUPERFAMILY | SSF53955 | Lysozyme-like | 19 | 139 | 2.95E-45 |
| 16 | g1245.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 15 | g1245.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 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