General information for g1949.t2
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.t2 | TTS | g1949.t2 | 14017988 | 14017988 |
| chr_3 | g1949 | g1949.t2 | isoform | g1949.t2 | 14019018 | 14020791 |
| chr_3 | g1949 | g1949.t2 | exon | g1949.t2.exon1 | 14019018 | 14020317 |
| chr_3 | g1949 | g1949.t2 | cds | g1949.t2.CDS1 | 14019960 | 14020317 |
| chr_3 | g1949 | g1949.t2 | exon | g1949.t2.exon2 | 14020377 | 14020591 |
| chr_3 | g1949 | g1949.t2 | cds | g1949.t2.CDS2 | 14020377 | 14020591 |
| chr_3 | g1949 | g1949.t2 | exon | g1949.t2.exon3 | 14020665 | 14020791 |
| chr_3 | g1949 | g1949.t2 | cds | g1949.t2.CDS3 | 14020665 | 14020682 |
| chr_3 | g1949 | g1949.t2 | TSS | g1949.t2 | 14021210 | 14021210 |
Sequences
>g1949.t2 Gene=g1949 Length=1642
TCCTGGAATTTTTCATGACAACATTTCTAGCATTAATCTAGAACACAATCAAATTGATAA
GATACCCTATGGAATTTTCTCAAGAGCAAAAGCTCTTACAAAATTAAATATGAAAGAGAA
CTCTTTGACACAATTACCGCTTGATCTCGGAACTTGGACTAATATGGTTGAATTGAATTT
AGGAACGAATGCAATTACAAAACTTCCAGATGATATTTCCAATCTACAACAACTCGAGAT
TTTGATTTTGTCAAATAATTTATTAAAAAAGATTCCTACAACAATTGGCAATTTAAGAAA
GTTACGAGTGCTAGATCTTGAGGAGAATCGTTTGGAGGGAACTATTCCTGCTGAGATTGG
TCTTTTACATGATCTACAAAAGTTGATATTACAATCTAATCAAATAACCGCTTTGCCGAG
ATCGATTGGTCATCTTTCGAGCTTAACATATTTGTCAGTGGGCGAAAATAATCTTCAGTA
CATCCCAGAAGAAATTGCAAATTTGGAAAACCTTGAATCGTTATACATCAATGATAATCC
CTTAATTAAATTGCCATTTGGCTTGGCATTGTGTCAAAATTTGGCCATCATGTCGATTGA
AAATTGCCCATTAAGTTCAATTCCTCAGGAAGTTGTAGCAGGTGGCCCTTCTCTTATAAT
ACAATATTTAAAATTGCATTCACCCTTTCGCCAAATGTGATTTACTAATGACATGACGAT
TCAAAGCCAAAAAAATAAATTTGGAGGCAGACTTAGTCGCCAACAACACGTAAGCTCATC
CTTCAGTAAATCACGTCCACTCTCTCAAAGTAAGTCGTTTACGAGTCTAAAAGAATTGAA
TAGTTACTATCAAAACTATTTTCGATTTGAGATTAAATGCGGAACACACTCATTTGTCTA
TGAGAAAAATGTTAATCGAAGCATAAGCCATTAAATGTTTTTACCTTCAACAATCTATCT
ACCTTACATACATCTTAAGGGAAAAAGTTTTGTTTTACAAAAAAAAGTTTTAGGAGTTGT
GTAGTTTCAAAATAGCACTTTACTTATTTATTTTCTTTCAAATTAATGTAGATTCATTGA
CTGTAATTAAGAAGTTTTCTAAAGTATATTTTTTGACAAAAATATTTAAAGAATGAATTT
CATTCACATACATAATAACACAACTCTTTGCATTTAATCTTGTAAATGTTGAGAGCTTAC
GATGATGAAAAGTTTAAATACATATATATTTAAGATATATCTTTCTATTGTCGTAATTGA
AATTGAATCCTAAAAAATCGTCATTGAAATCAGCGTGGCAAAAAACGCTGATTAAATTTC
ATTACTCAACTAAAACAATGAACTATAAAAATGTTTAAACCTATCTTCGCTTTAACGAAA
TAAAATTGAATACACATAAAAATATCTTAGCATATTGGAAAGATTAATGAAAAGATTTTC
TTTAAATATTGTAAAACATGATAAAAATAATGCATTACAACCTTGAACGATAAATAATAT
AAAATTTGTTTGTGAGAGAAATATTTACTTGCTCATTGCAATACTTGGTGATTATCATGT
CGACTGGTTTTTTTACTTTAATTTTTACCTCAATATAATATTTATTAACTAAAAACAAAC
ATGACTATTTATGAAATGATCG
>g1949.t2 Gene=g1949 Length=196
MKENSLTQLPLDLGTWTNMVELNLGTNAITKLPDDISNLQQLEILILSNNLLKKIPTTIG
NLRKLRVLDLEENRLEGTIPAEIGLLHDLQKLILQSNQITALPRSIGHLSSLTYLSVGEN
NLQYIPEEIANLENLESLYINDNPLIKLPFGLALCQNLAIMSIENCPLSSIPQEVVAGGP
SLIIQYLKLHSPFRQM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g1949.t2 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 1 | 80 | 0.000 |
| 17 | g1949.t2 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 81 | 189 | 0.000 |
| 3 | g1949.t2 | PANTHER | PTHR48051:SF9 | SHOC2, LEUCINE RICH REPEAT SCAFFOLD PROTEIN | 1 | 196 | 0.000 |
| 4 | g1949.t2 | PANTHER | PTHR48051 | - | 1 | 196 | 0.000 |
| 2 | g1949.t2 | Pfam | PF13855 | Leucine rich repeat | 18 | 75 | 0.000 |
| 1 | g1949.t2 | Pfam | PF13855 | Leucine rich repeat | 89 | 145 | 0.000 |
| 18 | g1949.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 18 | 39 | 6.287 |
| 21 | g1949.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 41 | 62 | 7.065 |
| 23 | g1949.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 64 | 86 | 6.742 |
| 20 | g1949.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 88 | 109 | 6.480 |
| 19 | g1949.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 111 | 132 | 6.041 |
| 22 | g1949.t2 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 134 | 155 | 6.572 |
| 12 | g1949.t2 | SMART | SM00369 | LRR_typ_2 | 16 | 38 | 130.000 |
| 8 | g1949.t2 | SMART | SM00364 | LRR_bac_2 | 39 | 58 | 16.000 |
| 11 | g1949.t2 | SMART | SM00369 | LRR_typ_2 | 39 | 61 | 6.100 |
| 10 | g1949.t2 | SMART | SM00369 | LRR_typ_2 | 62 | 85 | 54.000 |
| 7 | g1949.t2 | SMART | SM00364 | LRR_bac_2 | 86 | 105 | 72.000 |
| 15 | g1949.t2 | SMART | SM00369 | LRR_typ_2 | 86 | 108 | 2.300 |
| 6 | g1949.t2 | SMART | SM00364 | LRR_bac_2 | 109 | 128 | 32.000 |
| 14 | g1949.t2 | SMART | SM00369 | LRR_typ_2 | 109 | 131 | 6.300 |
| 9 | g1949.t2 | SMART | SM00364 | LRR_bac_2 | 132 | 151 | 130.000 |
| 13 | g1949.t2 | SMART | SM00369 | LRR_typ_2 | 132 | 155 | 20.000 |
| 5 | g1949.t2 | SUPERFAMILY | SSF52058 | L domain-like | 3 | 182 | 0.000 |
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.
