General information for g1949.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Leucine-rich repeat protein soc-2-like protein.
Parent gene
- The parent gene g1949 is located on chr_3: 14020665..14022125 (- 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 | g1949 | g1949.t3 | TTS | g1949.t3 | 14019662 | 14019662 |
| chr_3 | g1949 | g1949.t3 | isoform | g1949.t3 | 14020665 | 14022125 |
| chr_3 | g1949 | g1949.t3 | exon | g1949.t3.exon1 | 14020665 | 14020792 |
| chr_3 | g1949 | g1949.t3 | cds | g1949.t3.CDS1 | 14020665 | 14020792 |
| chr_3 | g1949 | g1949.t3 | exon | g1949.t3.exon2 | 14020856 | 14021142 |
| chr_3 | g1949 | g1949.t3 | cds | g1949.t3.CDS2 | 14020856 | 14021142 |
| chr_3 | g1949 | g1949.t3 | exon | g1949.t3.exon3 | 14021257 | 14021366 |
| chr_3 | g1949 | g1949.t3 | cds | g1949.t3.CDS3 | 14021257 | 14021366 |
| chr_3 | g1949 | g1949.t3 | exon | g1949.t3.exon4 | 14021435 | 14021541 |
| chr_3 | g1949 | g1949.t3 | cds | g1949.t3.CDS4 | 14021435 | 14021541 |
| chr_3 | g1949 | g1949.t3 | exon | g1949.t3.exon5 | 14021623 | 14021695 |
| chr_3 | g1949 | g1949.t3 | cds | g1949.t3.CDS5 | 14021623 | 14021695 |
| chr_3 | g1949 | g1949.t3 | exon | g1949.t3.exon6 | 14021823 | 14022125 |
| chr_3 | g1949 | g1949.t3 | cds | g1949.t3.CDS6 | 14021823 | 14022125 |
| chr_3 | g1949 | g1949.t3 | TSS | g1949.t3 | 14022364 | 14022364 |
Sequences
>g1949.t3 Gene=g1949 Length=1008
ATGGAAACTGGGATAAAGCAAGTGACTGTAAAACTTGATGCTAAGCAGTCAAAGCCAACA
AATACGAAAAAGAATAACAAATCACAACCCGATGTGGATTTAAATAAAGAATTTATTAAA
GCGAAAGATGAAGGAATAACAAGATTGAACTTATCAAAAAATAACATCACCATCGTTCCA
CCCTCTATTAAAGAATGTTCGCATTTAGTGGAGCTGTATCTTTATGGTAATAAAATTGCT
AGTTTGCCACCAGAAATTGGAATGTTAACGCAATTAAATGTGTTGGCTTTAAATGAAAAT
CAGTTGACTTCATTACCTGATACATTGCAAAATTTGACAAAATTAAAAGTTTTGGATCTT
CGCCATAACAAATTAGGCGAAGAAATTCCAGATGCTATATACAAATTAAAAAGCTTGACA
ACATTATATCTGCGTTTCAATCGAATTCGTAGTGTGAGTGAGGAAATTAGGAATTTAGAA
AAGCTAACAATGCTCAGCTTGCGTGAAAATAAAATTAAAAGTTTACCAAGAGCCATAGGA
TGTTTAGTAAATTTGGACATTTTAGACATCAGTCATAATCATTTAGAGCATTTACCTGAA
GAGATTGGAATGTGTAAAAATCTAAGTGCTTTAGATCTTCAACATAACGATCTAATTGAT
TTACCAGAGACAATTGGAAATTTAGTAAATTTGGCTAGACTTGGCTTACGCTACAATCGA
CTGACCCTCATCCCACAATCACTTAAAAATTGTTGCGCACTAGAGGAGTTTAATATTGAA
GGGAACTCAGTCTCAGAATTACCCGGAATTTTAGCGAATTTAACACTCTTAACGAGTATT
ACTCTATCGAGAAATTCTTTTACCAGTTTTCCTGCTGGTGGTCCTGGAATTTTTCATGAC
AACATTTCTAGCATTAATCTAGAACACAATCAAATTGATAAGATACCCTATGGAATTTTC
TCAAGAGCAAAAGCTCTTACAAAATTAAATATGAAAGAGAACTCTTTG
>g1949.t3 Gene=g1949 Length=336
METGIKQVTVKLDAKQSKPTNTKKNNKSQPDVDLNKEFIKAKDEGITRLNLSKNNITIVP
PSIKECSHLVELYLYGNKIASLPPEIGMLTQLNVLALNENQLTSLPDTLQNLTKLKVLDL
RHNKLGEEIPDAIYKLKSLTTLYLRFNRIRSVSEEIRNLEKLTMLSLRENKIKSLPRAIG
CLVNLDILDISHNHLEHLPEEIGMCKNLSALDLQHNDLIDLPETIGNLVNLARLGLRYNR
LTLIPQSLKNCCALEEFNIEGNSVSELPGILANLTLLTSITLSRNSFTSFPAGGPGIFHD
NISSINLEHNQIDKIPYGIFSRAKALTKLNMKENSL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 28 | g1949.t3 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 2 | 146 | 5.7E-36 |
| 26 | g1949.t3 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 147 | 239 | 3.6E-29 |
| 27 | g1949.t3 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 240 | 336 | 3.1E-16 |
| 25 | g1949.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 32 | - |
| 24 | g1949.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 13 | 28 | - |
| 3 | g1949.t3 | PANTHER | PTHR48051:SF9 | SHOC2, LEUCINE RICH REPEAT SCAFFOLD PROTEIN | 7 | 336 | 9.6E-103 |
| 4 | g1949.t3 | PANTHER | PTHR48051 | - | 7 | 336 | 9.6E-103 |
| 2 | g1949.t3 | Pfam | PF13855 | Leucine rich repeat | 67 | 125 | 2.0E-10 |
| 1 | g1949.t3 | Pfam | PF13855 | Leucine rich repeat | 138 | 195 | 1.4E-12 |
| 30 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 45 | 66 | 6.041 |
| 39 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 68 | 89 | 7.481 |
| 35 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 91 | 113 | 7.196 |
| 34 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 114 | 137 | 6.626 |
| 33 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 138 | 159 | 7.273 |
| 32 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 161 | 182 | 7.019 |
| 31 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 184 | 205 | 8.066 |
| 37 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 207 | 228 | 7.065 |
| 36 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 230 | 251 | 5.895 |
| 29 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 253 | 275 | 5.456 |
| 38 | g1949.t3 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 301 | 322 | 6.449 |
| 17 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 66 | 88 | 58.0 |
| 11 | g1949.t3 | SMART | SM00364 | LRR_bac_2 | 89 | 108 | 37.0 |
| 16 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 89 | 111 | 0.84 |
| 14 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 112 | 135 | 17.0 |
| 22 | g1949.t3 | SMART | SM00365 | LRR_sd22_2 | 112 | 131 | 15.0 |
| 10 | g1949.t3 | SMART | SM00364 | LRR_bac_2 | 136 | 155 | 110.0 |
| 13 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 136 | 158 | 1.4 |
| 23 | g1949.t3 | SMART | SM00365 | LRR_sd22_2 | 136 | 161 | 0.13 |
| 6 | g1949.t3 | SMART | SM00364 | LRR_bac_2 | 159 | 178 | 130.0 |
| 15 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 159 | 181 | 5.9 |
| 9 | g1949.t3 | SMART | SM00364 | LRR_bac_2 | 182 | 201 | 43.0 |
| 19 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 182 | 205 | 0.012 |
| 21 | g1949.t3 | SMART | SM00365 | LRR_sd22_2 | 182 | 200 | 380.0 |
| 8 | g1949.t3 | SMART | SM00364 | LRR_bac_2 | 205 | 224 | 91.0 |
| 7 | g1949.t3 | SMART | SM00364 | LRR_bac_2 | 228 | 247 | 110.0 |
| 18 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 228 | 251 | 17.0 |
| 12 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 274 | 300 | 9.0 |
| 20 | g1949.t3 | SMART | SM00369 | LRR_typ_2 | 301 | 322 | 200.0 |
| 5 | g1949.t3 | SUPERFAMILY | SSF52058 | L domain-like | 44 | 336 | 2.72E-64 |
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.
