General information for g1050.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ribosomal RNA-processing protein 7 homolog A.
Parent gene
- The parent gene g1050 is located on chr_3: 7841408..7844824 (- 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 | g1050 | g1050.t1 | TTS | g1050.t1 | 7840484 | 7840484 |
| chr_3 | g1050 | g1050.t1 | isoform | g1050.t1 | 7840514 | 7841408 |
| chr_3 | g1050 | g1050.t1 | exon | g1050.t1.exon1 | 7840514 | 7841316 |
| chr_3 | g1050 | g1050.t1 | cds | g1050.t1.CDS1 | 7840514 | 7841316 |
| chr_3 | g1050 | g1050.t1 | exon | g1050.t1.exon2 | 7841369 | 7841408 |
| chr_3 | g1050 | g1050.t1 | cds | g1050.t1.CDS2 | 7841369 | 7841408 |
| chr_3 | g1050 | g1050.t1 | TSS | g1050.t1 | NA | NA |
Sequences
>g1050.t1 Gene=g1050 Length=843
ATGAATTCAGAAACCAATAATAAACTTGAAGATTATAAAATTTTCACATTGAAATATTCA
GAAGAGAGTGATGAGAAATCTTCACATAGTATTTATGTGAAAAAATATAGATCAGAAAAG
AAATCTACAAGAAAACCTATTGGAAAAACAATAGTGGCTCTCAATATTCCTCCATATGCT
GATGAAACATCACTTTCAAACGTTTTCAGCATTATTGGTGAAGTTCAAAATGTCATTTTA
ATTGATTCATTTGCAAATGAACATAAAACTAAATATGAACTCCCTTCAAAATTCTTTAAA
CATAAATTACCTTTTAAATTTTTGATTGCATTTGTGATTTTTAAGAAATCCAGTTCAGTC
GATGTTTTATTTAATCAAAAAACTGTTGTTACATTACCTCCTTTGAGTTCAGAAGAACAA
CCGCTTCTAACTGGTGTTGCTAAATGGACAGCAGAGTACAATAGTCGATCAATTGATACG
GAAGAAATGCAGAAAGAAATTGATGAATACATGTTGCATTACGATAAAATAAAGCGTGCA
GAAGAGATGAATGGAGAAGATGAAGCTGATGATGATGGTTGGATAACAGTAGGAAAGAAA
GGTCATTATGCTGGATTTAAACAAAATGAAACAGTCGTGAATCGATTAGAGCAAAAAATT
GAAACTCAAAAGAAGAAAGCAAAGCAAATGTTGAAAACTAATTATCAGAAAGCATCAGGA
ATTTATTCATTTCAATTTAAAGAAGGAAAAAAACAAGAGCTGTTACAGTTGAGAAAGAAA
TTTCAAGATGATAAAACAAAATTGCAAGCTCTTAGAACAAGTAGAAAATTTAAACCTTAT
TGA
>g1050.t1 Gene=g1050 Length=280
MNSETNNKLEDYKIFTLKYSEESDEKSSHSIYVKKYRSEKKSTRKPIGKTIVALNIPPYA
DETSLSNVFSIIGEVQNVILIDSFANEHKTKYELPSKFFKHKLPFKFLIAFVIFKKSSSV
DVLFNQKTVVTLPPLSSEEQPLLTGVAKWTAEYNSRSIDTEEMQKEIDEYMLHYDKIKRA
EEMNGEDEADDDGWITVGKKGHYAGFKQNETVVNRLEQKIETQKKKAKQMLKTNYQKASG
IYSFQFKEGKKQELLQLRKKFQDDKTKLQALRTSRKFKPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1050.t1 | CDD | cd12951 | RRP7_Rrp7A | 145 | 280 | 4.41542E-39 |
| 5 | g1050.t1 | Coils | Coil | Coil | 206 | 233 | - |
| 2 | g1050.t1 | PANTHER | PTHR13191 | RIBOSOMAL RNA PROCESSING PROTEIN 7-RELATED | 7 | 280 | 1.4E-37 |
| 3 | g1050.t1 | PANTHER | PTHR13191:SF0 | RIBOSOMAL RNA-PROCESSING PROTEIN 7 HOMOLOG A-RELATED | 7 | 280 | 1.4E-37 |
| 1 | g1050.t1 | Pfam | PF12923 | Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain | 156 | 280 | 3.8E-23 |
| 4 | g1050.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 30 | 85 | 5.81E-5 |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14545 (ribosomal RNA-processing protein 7)
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.
