General information for g2562.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein spitz.
Parent gene
- The parent gene g2562 is located on chr_3: 18701405..18706756 (+ 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 | g2562 | g2562.t1 | TSS | g2562.t1 | 18700926 | 18700926 |
| chr_3 | g2562 | g2562.t1 | isoform | g2562.t1 | 18701405 | 18706756 |
| chr_3 | g2562 | g2562.t1 | exon | g2562.t1.exon1 | 18701405 | 18701468 |
| chr_3 | g2562 | g2562.t1 | cds | g2562.t1.CDS1 | 18701405 | 18701468 |
| chr_3 | g2562 | g2562.t1 | exon | g2562.t1.exon2 | 18703854 | 18703976 |
| chr_3 | g2562 | g2562.t1 | cds | g2562.t1.CDS2 | 18703854 | 18703976 |
| chr_3 | g2562 | g2562.t1 | exon | g2562.t1.exon3 | 18706133 | 18706313 |
| chr_3 | g2562 | g2562.t1 | cds | g2562.t1.CDS3 | 18706133 | 18706313 |
| chr_3 | g2562 | g2562.t1 | exon | g2562.t1.exon4 | 18706436 | 18706497 |
| chr_3 | g2562 | g2562.t1 | cds | g2562.t1.CDS4 | 18706436 | 18706497 |
| chr_3 | g2562 | g2562.t1 | exon | g2562.t1.exon5 | 18706572 | 18706756 |
| chr_3 | g2562 | g2562.t1 | cds | g2562.t1.CDS5 | 18706572 | 18706756 |
| chr_3 | g2562 | g2562.t1 | TTS | g2562.t1 | 18707072 | 18707072 |
Sequences
>g2562.t1 Gene=g2562 Length=615
ATGAAAAGGTACTCGCTAAGCAACCTCAATGTTGGATTACAATTTTTTATCGATCAAGTG
TCAGACTTTAGAAAGAAGAATTTCAATATCCAAAAGACGCTCAACGCATCAAGCCGTTCC
AGTTCCAAAGTTACGGCCTCGGCTTTCCTGATAGTCTTAATATTTAGTGCAATTTGTGAT
GTTACTGATGCTTGCAGAAGTCGTACAGTTTACAAGCCAAGAACAACACAAGCGCCAACC
ACAAGTCCACGACCAAATATTACATTCCACACTTATAAATGTCCTGAAGCATATGCAAAT
TGGTATTGCCTCAATGGTGCAACATGCTTTGCTGTTAAAATTGGAATGGAAGTTCTTTAT
AATTGCGAATGCAAAGATGGCTATATTGGACCAAGATGTGATTACAAAGATCTCGATGGC
TCATATTTATCTGCAAGATCACGCGTGATGCTCGAAACAGCAAGTATCGCTGGAGGTGCC
GTTGCTGCCTTGCTCTTAGCATGCATTGTCGGTATTTTTGTCTACCTCAAAAAGCACACA
ACCAAACCATGTGAGTTTGAAGTCGAAAGTCAAAAACCAAATCACAAAAATTGCAACGAA
TGTCAAAAATTTTAA
>g2562.t1 Gene=g2562 Length=204
MKRYSLSNLNVGLQFFIDQVSDFRKKNFNIQKTLNASSRSSSKVTASAFLIVLIFSAICD
VTDACRSRTVYKPRTTQAPTTSPRPNITFHTYKCPEAYANWYCLNGATCFAVKIGMEVLY
NCECKDGYIGPRCDYKDLDGSYLSARSRVMLETASIAGGAVAALLLACIVGIFVYLKKHT
TKPCEFEVESQKPNHKNCNECQKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g2562.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 88 | 139 | 5.9E-24 |
| 2 | g2562.t1 | PANTHER | PTHR12332 | KEREN-RELATED | 48 | 181 | 2.9E-52 |
| 1 | g2562.t1 | Pfam | PF00008 | EGF-like domain | 94 | 132 | 1.7E-6 |
| 7 | g2562.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 43 | - |
| 9 | g2562.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 65 | - |
| 5 | g2562.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 66 | 155 | - |
| 8 | g2562.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 156 | 176 | - |
| 6 | g2562.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 177 | 204 | - |
| 11 | g2562.t1 | ProSitePatterns | PS01186 | EGF-like domain signature 2. | 122 | 133 | - |
| 12 | g2562.t1 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 122 | 133 | - |
| 13 | g2562.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 90 | 134 | 11.756 |
| 3 | g2562.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 92 | 138 | 1.07E-7 |
| 10 | g2562.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 154 | 176 | - |
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:0048018 | receptor ligand activity | MF |
| GO:0007173 | epidermal growth factor receptor signaling pathway | BP |
| GO:0005154 | epidermal growth factor receptor binding | MF |
KEGG
Orthology
- This transcript has been annotated with K16691 (keren)
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