Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Lysozyme.

Parent gene

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 g1248 g1248.t2 TSS g1248.t2 9120697 9120697
chr_3 g1248 g1248.t2 isoform g1248.t2 9120736 9121220
chr_3 g1248 g1248.t2 exon g1248.t2.exon1 9120736 9121025
chr_3 g1248 g1248.t2 cds g1248.t2.CDS1 9120736 9121025
chr_3 g1248 g1248.t2 exon g1248.t2.exon2 9121081 9121220
chr_3 g1248 g1248.t2 cds g1248.t2.CDS2 9121081 9121090
chr_3 g1248 g1248.t2 TTS g1248.t2 9121369 9121369

Sequences

>g1248.t2 Gene=g1248 Length=430
ATGAAAATTTTTATTATATCATTTTTGCTTTTTGCAATATTTGCATTTTCTGAAGCAAAA
GTTTTCACAAAATGTGAATTAGTCAAGGCACTTTATAAAGCTGGCATACCAAAATCAAAG
CTACGTGATTGGGCTTGTTTAGTACAACATGAAAGTAGCTACAACTCAAAAGCAAAAGGA
GGACCGAACAAAAATGGCTCATATGACTATGGGATTTTTCAAATCAATTCAAAATATTGG
TGTGGAATTGGAAAAGTTGGTGGAGATTGCAAAATAAATTGCAATTGTGACATTAATTAA
TAATGACATCACTGATGACATCAAATGTGCTAAAACTATCTATAATCGACATAATTTTAC
AGCATGGTATGGCTGGAACAGTAAATGCAAAGAAAAGAAACTTCCTTCAATCAGTGAATG
CACACTTTAA

>g1248.t2 Gene=g1248 Length=99
MKIFIISFLLFAIFAFSEAKVFTKCELVKALYKAGIPKSKLRDWACLVQHESSYNSKAKG
GPNKNGSYDYGIFQINSKYWCGIGKVGGDCKINCNCDIN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1248.t2 Gene3D G3DSA:1.10.530.10 - 16 99 1.3E-28
2 g1248.t2 PANTHER PTHR11407 LYSOZYME C 1 95 3.0E-29
3 g1248.t2 PANTHER PTHR11407:SF36 GEO02684P1-RELATED 1 95 3.0E-29
6 g1248.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 22 32 3.1E-9
5 g1248.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 39 48 3.1E-9
7 g1248.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 67 83 3.1E-9
4 g1248.t2 PRINTS PR00135 Lysozyme/alpha-lactalbumin superfamily signature 88 97 3.1E-9
1 g1248.t2 Pfam PF00062 C-type lysozyme/alpha-lactalbumin family 20 95 2.2E-18
12 g1248.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
13 g1248.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
14 g1248.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
15 g1248.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
11 g1248.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 99 -
18 g1248.t2 ProSiteProfiles PS51348 Glycosyl hydrolases family 22 (GH22) domain profile. 20 99 24.729
17 g1248.t2 SMART SM00263 lysozyme-fin 20 99 2.3E-11
8 g1248.t2 SUPERFAMILY SSF53955 Lysozyme-like 20 95 6.7E-29
9 g1248.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
16 g1248.t2 SignalP_GRAM_NEGATIVE 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

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed