General information for g3089.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Leucine-rich repeat-containing protein 15.
Parent gene
- The parent gene g3089 is located on chr_3: 22638452..22639446 (+ 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 | g3089 | g3089.t1 | TSS | g3089.t1 | 22638244 | 22638244 |
| chr_3 | g3089 | g3089.t1 | isoform | g3089.t1 | 22638268 | 22639446 |
| chr_3 | g3089 | g3089.t1 | exon | g3089.t1.exon1 | 22638268 | 22639446 |
| chr_3 | g3089 | g3089.t1 | cds | g3089.t1.CDS1 | 22638268 | 22639446 |
| chr_3 | g3089 | g3089.t1 | TTS | g3089.t1 | 22639493 | 22639493 |
Sequences
>g3089.t1 Gene=g3089 Length=1179
ATGAAGTTGACATTTTTCGTAATTTTGTTAATTGTTATAATTAAAAGTGTTTCATCGCAA
GTTCTTTGTTTATTTGCACAAGTTAATGGTTTATACACTTGCACAGCAACTATAATTAAT
CCATTAGGATTAAACAATTTCACTCAAGTTGAAGGCATACATTTTACAGGCGGAACTGAT
GAAGATGTCGTAAGAATTGAGAGAAATGCAGTTTCAAATACACTGAATTTTCCATCAATA
TTTTGTAATCAATTTGGAAACACTGAATCAATTATCATTGATAATATTGGCATTGAAAGA
ATTGATGAAAATGCATTTGCTGATTGTCGTGATCTTGAATATTTGTTATTGCAATCTAAT
AGACTACGAGAAATTCATGAAAATGCATTCAGTGAAAATTTGCAATTATCAATTTTGGAT
TTATCGAACAATCAATTAATTCGATTACCTGGAAATTTGTTTAGAAATCAAATTAATTTG
TATTTTCTCCAACTTGCTTCAAATCAACTTCAAGAGCTACCAAGCGATATTTTCAATCAA
TTGTCAGAACTTGGAATGTTAAATTTAGATTCAAATCAACTACAAGATTTGCCTGAAGGA
ATTTTCGATAACCTACCAAATCTTTATTATCTTTCATTTTCATTTAACCAAATTGTAAAA
CTAAGAGAAAATTTGATTGATAAACTTTACAGCATTCAAAATTTTTTGGCTCCTTTCAAT
CAAATCATTTATATTCCACGAAACTTCTTTGATGGAAATCCTTATCTTTCGAGCATTATT
ATCAGTGGAAATAATTTAACAATACTTGAATTAAATCCTATTCCAATGCTTTCTGATTTT
TGGTTCGAACATAATCAAATTAATGCAATTGATGAGAGAATTTTTAATAATGTGACACTT
AGATCGTTAAATGGCGGTCCAAATCCATGTGCTGATAGAAATGGCATAATTTCAAATCCA
ACAAATGATGACATCAGAGCAGCGTTGCATAGATGTTTTGATAATTTCAATCCAATTGAA
ACGACAACAACACCTGGAGAAGAAATTACAAAACCAACAACAGAGCCAAATGGGTGTGAA
GTTGGAAATATTGAAGAAAGAATTTGTCAATTGGAGGCTGAAAATGCCGAATTGAGAGCG
AGACTGGAATATTTGGAGAAAATTGTTTTAGGTCGTTAA
>g3089.t1 Gene=g3089 Length=392
MKLTFFVILLIVIIKSVSSQVLCLFAQVNGLYTCTATIINPLGLNNFTQVEGIHFTGGTD
EDVVRIERNAVSNTLNFPSIFCNQFGNTESIIIDNIGIERIDENAFADCRDLEYLLLQSN
RLREIHENAFSENLQLSILDLSNNQLIRLPGNLFRNQINLYFLQLASNQLQELPSDIFNQ
LSELGMLNLDSNQLQDLPEGIFDNLPNLYYLSFSFNQIVKLRENLIDKLYSIQNFLAPFN
QIIYIPRNFFDGNPYLSSIIISGNNLTILELNPIPMLSDFWFEHNQINAIDERIFNNVTL
RSLNGGPNPCADRNGIISNPTNDDIRAALHRCFDNFNPIETTTTPGEEITKPTTEPNGCE
VGNIEERICQLEAENAELRARLEYLEKIVLGR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g3089.t1 | CDD | cd14686 | bZIP | 363 | 389 | 0.00538051 |
| 9 | g3089.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 59 | 167 | 1.5E-16 |
| 10 | g3089.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 168 | 324 | 1.9E-24 |
| 3 | g3089.t1 | PANTHER | PTHR45842:SF3 | LEUCINE-RICH REPEAT AND FIBRONECTIN TYPE-III DOMAIN-CONTAINING PROTEIN 4 | 98 | 267 | 5.8E-36 |
| 5 | g3089.t1 | PANTHER | PTHR45842 | SYNAPTIC ADHESION-LIKE MOLECULE SALM | 98 | 267 | 5.8E-36 |
| 2 | g3089.t1 | PANTHER | PTHR45842:SF3 | LEUCINE-RICH REPEAT AND FIBRONECTIN TYPE-III DOMAIN-CONTAINING PROTEIN 4 | 136 | 310 | 5.8E-36 |
| 4 | g3089.t1 | PANTHER | PTHR45842 | SYNAPTIC ADHESION-LIKE MOLECULE SALM | 136 | 310 | 5.8E-36 |
| 1 | g3089.t1 | Pfam | PF13306 | BspA type Leucine rich repeat region (6 copies) | 80 | 208 | 6.6E-13 |
| 12 | g3089.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 13 | g3089.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 14 | g3089.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 15 | g3089.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 11 | g3089.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 392 | - |
| 24 | g3089.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 111 | 132 | 6.849 |
| 23 | g3089.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 135 | 156 | 7.427 |
| 26 | g3089.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 159 | 180 | 6.772 |
| 25 | g3089.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 183 | 204 | 6.68 |
| 27 | g3089.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 207 | 229 | 5.941 |
| 20 | g3089.t1 | SMART | SM00369 | LRR_typ_2 | 109 | 132 | 11.0 |
| 17 | g3089.t1 | SMART | SM00369 | LRR_typ_2 | 135 | 156 | 9.7 |
| 22 | g3089.t1 | SMART | SM00369 | LRR_typ_2 | 158 | 180 | 14.0 |
| 19 | g3089.t1 | SMART | SM00369 | LRR_typ_2 | 181 | 204 | 7.8E-4 |
| 18 | g3089.t1 | SMART | SM00369 | LRR_typ_2 | 205 | 228 | 9.7 |
| 21 | g3089.t1 | SMART | SM00369 | LRR_typ_2 | 274 | 297 | 60.0 |
| 6 | g3089.t1 | SUPERFAMILY | SSF52058 | L domain-like | 77 | 308 | 3.06E-35 |
| 8 | g3089.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 7 | g3089.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 26 | - |
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:0005515 | protein binding | 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. There were no conditions that were differentially expressed