General information for g11970.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein lap4.
Parent gene
- The parent gene g11970 is located on chr_1: 20007751..20020803 (+ 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_1 | g11970 | g11970.t8 | TSS | g11970.t8 | 19963419 | 19963419 |
| chr_1 | g11970 | g11970.t8 | isoform | g11970.t8 | 19964332 | 19974145 |
| chr_1 | g11970 | g11970.t8 | exon | g11970.t8.exon1 | 19964332 | 19964493 |
| chr_1 | g11970 | g11970.t8 | cds | g11970.t8.CDS1 | 19964332 | 19964493 |
| chr_1 | g11970 | g11970.t8 | exon | g11970.t8.exon2 | 19969370 | 19969487 |
| chr_1 | g11970 | g11970.t8 | cds | g11970.t8.CDS2 | 19969370 | 19969487 |
| chr_1 | g11970 | g11970.t8 | exon | g11970.t8.exon3 | 19973977 | 19974145 |
| chr_1 | g11970 | g11970.t8 | cds | g11970.t8.CDS3 | 19973977 | 19974143 |
| chr_1 | g11970 | g11970.t8 | TTS | g11970.t8 | NA | NA |
Sequences
>g11970.t8 Gene=g11970 Length=449
ATGTTTAAGTGCATTCCCATATTCAAAGGATGTAATCGACAAGTGGAGTTTGTGGATAAA
AGACACTGCTCCTTACCAAATGTTCCCGAGGAAATTTTACGCTATTCAAGGAGTCTCGAG
GAATTGCTACTTGATGCAAATCATATTCGAGATTTGCCCAAGAATTTTTTCCGATTACAT
CGATTACGAAAGCTCGGCCTGAGTGACAATGAAATTCATAAACTTCCACCTGATATACAA
AATTTTGAAAATCTTGTAGAATTAGACGTATCAAGAAATGATATTCCTGACATTCCAGAT
GACATTCGCCATTTACGGCTTTTACAGATTGCTGATTTCAGCTCAAATCCTATTCCAAAA
TTACCAGCTGGTTTCTCACAGCTTAAAAGTTTGACAATATTAGGATTAAATGACATGTCC
TTGACCTCATTGCCAGCTGATTTTGGATG
>g11970.t8 Gene=g11970 Length=149
MFKCIPIFKGCNRQVEFVDKRHCSLPNVPEEILRYSRSLEELLLDANHIRDLPKNFFRLH
RLRKLGLSDNEIHKLPPDIQNFENLVELDVSRNDIPDIPDDIRHLRLLQIADFSSNPIPK
LPAGFSQLKSLTILGLNDMSLTSLPADFG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11970.t8 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 8 | 149 | 0.000 |
| 2 | g11970.t8 | PANTHER | PTHR23119:SF44 | PROTEIN SCRIBBLE HOMOLOG | 1 | 149 | 0.000 |
| 3 | g11970.t8 | PANTHER | PTHR23119 | DISCS LARGE | 1 | 149 | 0.000 |
| 1 | g11970.t8 | Pfam | PF13855 | Leucine rich repeat | 37 | 95 | 0.000 |
| 10 | g11970.t8 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 38 | 59 | 6.942 |
| 12 | g11970.t8 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 61 | 82 | 6.888 |
| 11 | g11970.t8 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 84 | 105 | 7.596 |
| 13 | g11970.t8 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 107 | 129 | 4.932 |
| 6 | g11970.t8 | SMART | SM00369 | LRR_typ_2 | 37 | 58 | 92.000 |
| 8 | g11970.t8 | SMART | SM00369 | LRR_typ_2 | 59 | 81 | 2.200 |
| 7 | g11970.t8 | SMART | SM00369 | LRR_typ_2 | 82 | 104 | 17.000 |
| 5 | g11970.t8 | SMART | SM00369 | LRR_typ_2 | 105 | 128 | 190.000 |
| 4 | g11970.t8 | SUPERFAMILY | SSF52058 | L domain-like | 5 | 146 | 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. There were no conditions that were differentially expressed