General information for g2561.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 g2561 is located on chr_3: 18681782..18683948 (- 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 | g2561 | g2561.t1 | isoform | g2561.t1 | 18681782 | 18683948 |
| chr_3 | g2561 | g2561.t1 | exon | g2561.t1.exon1 | 18681782 | 18682023 |
| chr_3 | g2561 | g2561.t1 | cds | g2561.t1.CDS1 | 18681782 | 18682023 |
| chr_3 | g2561 | g2561.t1 | exon | g2561.t1.exon2 | 18682098 | 18682159 |
| chr_3 | g2561 | g2561.t1 | cds | g2561.t1.CDS2 | 18682098 | 18682159 |
| chr_3 | g2561 | g2561.t1 | exon | g2561.t1.exon3 | 18682326 | 18682506 |
| chr_3 | g2561 | g2561.t1 | cds | g2561.t1.CDS3 | 18682326 | 18682506 |
| chr_3 | g2561 | g2561.t1 | exon | g2561.t1.exon4 | 18683903 | 18683948 |
| chr_3 | g2561 | g2561.t1 | cds | g2561.t1.CDS4 | 18683903 | 18683948 |
| chr_3 | g2561 | g2561.t1 | TSS | g2561.t1 | NA | NA |
| chr_3 | g2561 | g2561.t1 | TTS | g2561.t1 | NA | NA |
Sequences
>g2561.t1 Gene=g2561 Length=531
ATGCATTTAGTCATATTTTTACTTCTAATTTCTTTTAATGTTACAGATGCTTGCAGAAGT
CGTACAGTTTACAAGCCAAGAACAACACATGCGCCAACCACAAGTCCACGACCAAATATT
ACATTCCACACTTATAAATGTCCTGAAGCATATGCAAATTGGTATTGCCTCAATGGTGCA
ACATGCTTTGCTGTTAAAATTGGAATGGAAGTTCTTTATAATTGCGAATGCAAAGATGGC
TATATTGGACCAAGATGTGATTACAAAGATCTCGATGGCTCATATTTATCTGCAAGATCA
CGCGTGATGCTCGAAACAGCAAGTATCGCTGGAGGTGCCGTTGCTGCCTTGCTCTTAGCA
TGCATTGTCGGTATTTTTGTCTACCTCAAAAAGCACACAACCAAACCATGTGAGTTTGAA
GTCGAAAGTCAAAAGATAAATCACCATCACGACATAATTAAGCTGCATCGATATCATAGT
TGTCAAATTTCTGATCAGTTCACGATAGTCATCAAATATCACAATGGATGA
>g2561.t1 Gene=g2561 Length=176
MHLVIFLLLISFNVTDACRSRTVYKPRTTHAPTTSPRPNITFHTYKCPEAYANWYCLNGA
TCFAVKIGMEVLYNCECKDGYIGPRCDYKDLDGSYLSARSRVMLETASIAGGAVAALLLA
CIVGIFVYLKKHTTKPCEFEVESQKINHHHDIIKLHRYHSCQISDQFTIVIKYHNG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2561.t1 | CDD | cd00054 | EGF_CA | 56 | 86 | 0.00878548 |
| 5 | g2561.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 41 | 92 | 4.5E-24 |
| 2 | g2561.t1 | PANTHER | PTHR12332 | KEREN-RELATED | 4 | 134 | 3.6E-52 |
| 1 | g2561.t1 | Pfam | PF00008 | EGF-like domain | 47 | 85 | 1.4E-6 |
| 8 | g2561.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 9 | g2561.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 10 | g2561.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 12 | - |
| 12 | g2561.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 7 | g2561.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 108 | - |
| 11 | g2561.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 109 | 129 | - |
| 6 | g2561.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 130 | 176 | - |
| 15 | g2561.t1 | ProSitePatterns | PS01186 | EGF-like domain signature 2. | 75 | 86 | - |
| 16 | g2561.t1 | ProSitePatterns | PS00022 | EGF-like domain signature 1. | 75 | 86 | - |
| 17 | g2561.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 43 | 87 | 11.756 |
| 3 | g2561.t1 | SUPERFAMILY | SSF57196 | EGF/Laminin | 45 | 91 | 8.38E-8 |
| 4 | g2561.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
| 14 | g2561.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 107 | 129 | - |
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