General information for g13380.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative H/ACA ribonucleoprotein complex subunit 2-like protein.
Parent gene
- The parent gene g13380 is located on chr_1: 29613965..29614469 (- 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 | g13380 | g13380.t1 | TTS | g13380.t1 | 29613895 | 29613895 |
| chr_1 | g13380 | g13380.t1 | isoform | g13380.t1 | 29613965 | 29614469 |
| chr_1 | g13380 | g13380.t1 | exon | g13380.t1.exon1 | 29613965 | 29614359 |
| chr_1 | g13380 | g13380.t1 | cds | g13380.t1.CDS1 | 29613965 | 29614359 |
| chr_1 | g13380 | g13380.t1 | exon | g13380.t1.exon2 | 29614421 | 29614469 |
| chr_1 | g13380 | g13380.t1 | cds | g13380.t1.CDS2 | 29614421 | 29614469 |
| chr_1 | g13380 | g13380.t1 | TSS | g13380.t1 | 29614579 | 29614579 |
Sequences
>g13380.t1 Gene=g13380 Length=444
ATGAAAGCAGAAGAAAGCACTACCAAAATTAAATTAGAAGACAATTATGATGAAAAAATC
TTAAATGTCAATAAAATCTCTCAACCTCTTGCGTCAAGAAAATTAGCAAAGAAAATATAT
AAATTAATCAAAAAGGCATCAAAAGAACGTACAAAGAATATTATCAATGGATTAAAAGAT
GTTCAAACAAGAATTCGCAAGGGTGAAAGAGGAATTACAATCTTCGCCGGAGATGTTTTT
CCAGTGGATATTATTTGTCATTTACCGGCAGTTTGTGAAGAAAAAGATATTTCTTACTGC
TATACACCAAGTCGACAAGATTTAGGAACAGCAATGGGTGTAAAGAGAGGATCAATAGTA
CTCATGATTCGTGAAAATGCAGATTATAAAGACCTATATGATGAAGTCAAAGCTGAACTT
AAAACACTATCTACACCACTCTAG
>g13380.t1 Gene=g13380 Length=147
MKAEESTTKIKLEDNYDEKILNVNKISQPLASRKLAKKIYKLIKKASKERTKNIINGLKD
VQTRIRKGERGITIFAGDVFPVDIICHLPAVCEEKDISYCYTPSRQDLGTAMGVKRGSIV
LMIRENADYKDLYDEVKAELKTLSTPL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g13380.t1 | Gene3D | G3DSA:3.30.1330.30 | - | 21 | 144 | 0 |
| 2 | g13380.t1 | PANTHER | PTHR23105 | RIBOSOMAL PROTEIN L7AE FAMILY MEMBER | 12 | 147 | 0 |
| 3 | g13380.t1 | PANTHER | PTHR23105:SF129 | H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 2 | 12 | 147 | 0 |
| 6 | g13380.t1 | PRINTS | PR00881 | Ribosomal protein L7A/RS6 family signature | 54 | 68 | 0 |
| 5 | g13380.t1 | PRINTS | PR00881 | Ribosomal protein L7A/RS6 family signature | 73 | 86 | 0 |
| 4 | g13380.t1 | PRINTS | PR00881 | Ribosomal protein L7A/RS6 family signature | 89 | 99 | 0 |
| 7 | g13380.t1 | PRINTS | PR00881 | Ribosomal protein L7A/RS6 family signature | 99 | 113 | 0 |
| 1 | g13380.t1 | Pfam | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | 38 | 132 | 0 |
| 8 | g13380.t1 | SUPERFAMILY | SSF55315 | L30e-like | 17 | 142 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K11129 (H/ACA ribonucleoprotein complex subunit 2)
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.
