General information for g8476.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 g8476 is located on chr_2: 30884823..30885328 (+ 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_2 | g8476 | g8476.t1 | TSS | g8476.t1 | 30884803 | 30884803 |
| chr_2 | g8476 | g8476.t1 | isoform | g8476.t1 | 30884823 | 30885328 |
| chr_2 | g8476 | g8476.t1 | exon | g8476.t1.exon1 | 30884823 | 30885105 |
| chr_2 | g8476 | g8476.t1 | cds | g8476.t1.CDS1 | 30884823 | 30885105 |
| chr_2 | g8476 | g8476.t1 | exon | g8476.t1.exon2 | 30885165 | 30885328 |
| chr_2 | g8476 | g8476.t1 | cds | g8476.t1.CDS2 | 30885165 | 30885328 |
| chr_2 | g8476 | g8476.t1 | TTS | g8476.t1 | 30885403 | 30885403 |
Sequences
>g8476.t1 Gene=g8476 Length=447
ATGAAATCAGTTGTGGCTTTTATATTTCTAATCAGTTTTAATTTGGCAAGTGCTAAAATA
TTTTTAAATTGTGAATTCGCTAAAGAACTCGGTAAAAATGAAGCAATTGAAAGAGTATAT
ATTCCTCATTGGGTGTGCTTAGCACAGGGTGAAAGTCAATTAAATACGAGTAAACTTGTT
AATTATCCAAATCAATCATCAAGTTATGGAATTTTTCAGATTAACAGCAAGGAACAATGT
GGAAAGGATAAAAAGGGAGGTTTTTGTAATATAAAATGTTCAGATCTTCTAGATGATGAC
ATAAAAGATGATATAAAATGTGCAAAAGTGATATTTGATCGCAGTGGATTCAACAATTGG
AAGTCTTGGCAAAACAGATGCAAGTCAACAAGTACAATTGATAAAAATAAAGCGCTTCCA
AATCTTGTCAATTGTCAGTATAAATAA
>g8476.t1 Gene=g8476 Length=148
MKSVVAFIFLISFNLASAKIFLNCEFAKELGKNEAIERVYIPHWVCLAQGESQLNTSKLV
NYPNQSSSYGIFQINSKEQCGKDKKGGFCNIKCSDLLDDDIKDDIKCAKVIFDRSGFNNW
KSWQNRCKSTSTIDKNKALPNLVNCQYK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g8476.t1 | Gene3D | G3DSA:1.10.530.10 | - | 17 | 143 | 1.1E-38 |
| 2 | g8476.t1 | PANTHER | PTHR11407 | LYSOZYME C | 4 | 130 | 2.4E-41 |
| 3 | g8476.t1 | PANTHER | PTHR11407:SF63 | LYSOZYME | 4 | 130 | 2.4E-41 |
| 10 | g8476.t1 | PRINTS | PR00137 | Lysozyme signature | 20 | 38 | 1.6E-5 |
| 7 | g8476.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 21 | 31 | 2.6E-17 |
| 4 | g8476.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 39 | 48 | 2.6E-17 |
| 6 | g8476.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 66 | 82 | 2.6E-17 |
| 11 | g8476.t1 | PRINTS | PR00137 | Lysozyme signature | 83 | 93 | 1.6E-5 |
| 9 | g8476.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 87 | 96 | 2.6E-17 |
| 13 | g8476.t1 | PRINTS | PR00137 | Lysozyme signature | 94 | 109 | 1.6E-5 |
| 8 | g8476.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 97 | 112 | 2.6E-17 |
| 12 | g8476.t1 | PRINTS | PR00137 | Lysozyme signature | 115 | 124 | 1.6E-5 |
| 5 | g8476.t1 | PRINTS | PR00135 | Lysozyme/alpha-lactalbumin superfamily signature | 116 | 127 | 2.6E-17 |
| 1 | g8476.t1 | Pfam | PF00062 | C-type lysozyme/alpha-lactalbumin family | 20 | 129 | 1.6E-28 |
| 19 | g8476.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 20 | g8476.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 21 | g8476.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 22 | g8476.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 18 | g8476.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 148 | - |
| 24 | g8476.t1 | ProSitePatterns | PS00128 | Glycosyl hydrolases family 22 (GH22) domain signature. | 89 | 107 | - |
| 26 | g8476.t1 | ProSiteProfiles | PS51348 | Glycosyl hydrolases family 22 (GH22) domain profile. | 19 | 148 | 29.118 |
| 25 | g8476.t1 | SMART | SM00263 | lysozyme-fin | 19 | 146 | 1.6E-32 |
| 14 | g8476.t1 | SUPERFAMILY | SSF53955 | Lysozyme-like | 18 | 130 | 5.32E-37 |
| 16 | g8476.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 23 | g8476.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 15 | g8476.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 27 | - |
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 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.
