General information for g5123.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 39S ribosomal protein L21, mitochondrial.
Parent gene
- The parent gene g5123 is located on chr_2: 7172674..7173535 (+ 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_2 | g5123 | g5123.t1 | TSS | g5123.t1 | 7171962 | 7171962 |
| chr_2 | g5123 | g5123.t1 | isoform | g5123.t1 | 7172035 | 7172674 |
| chr_2 | g5123 | g5123.t1 | exon | g5123.t1.exon1 | 7172035 | 7172095 |
| chr_2 | g5123 | g5123.t1 | cds | g5123.t1.CDS1 | 7172035 | 7172095 |
| chr_2 | g5123 | g5123.t1 | exon | g5123.t1.exon2 | 7172151 | 7172674 |
| chr_2 | g5123 | g5123.t1 | cds | g5123.t1.CDS2 | 7172151 | 7172674 |
| chr_2 | g5123 | g5123.t1 | TTS | g5123.t1 | 7172729 | 7172729 |
Sequences
>g5123.t1 Gene=g5123 Length=585
ATGTTTCTTAACAAAATAATAGGTTTAGCTAGAAGCCCAACGAGTGTAAATCAATTATCA
AATCTTTTTCAAAGATGCTTAATATCATCAACAAGCGCATTTCAAAATAAACTAACGCCA
GCACAGTCATTAGAAGTATCAAAATACGATGAAAGGAAGGATCCAGTAAAAAATATAAAT
GAAATGATCAAGAATGATGAAGCCGGAAGATTGTTTGCAGTTGTTCATATTTGTGGAAAA
CAATTTAAAGTGACAGCGGGCGATATAATTCTTATTGAAGGCCATTGGGAGCCAAGTAAT
GGTGATGAATTAAGATTAGAGAAAGTGCTTCTATGTGGATCACAAGATTTCACTCTAATC
GGACGTCCTATCCTTCAAAAAGACCTCGTCAATGTTCAGGCAACTGTTATTGAAAAATCA
CTTTCACACACAAGAACTCATTTCAAATTCAAGAAACGAAAGCAGTATAGAAGAATCAAT
TTTCAACGACAGCCAACAACTGTTTTGCGAATCAACTCAATAGAAATTAAAAATCTGGTT
AATCAAAATAAGAATGCTGAAAGTTTAGAAAATGTCTTCTATTGA
>g5123.t1 Gene=g5123 Length=194
MFLNKIIGLARSPTSVNQLSNLFQRCLISSTSAFQNKLTPAQSLEVSKYDERKDPVKNIN
EMIKNDEAGRLFAVVHICGKQFKVTAGDIILIEGHWEPSNGDELRLEKVLLCGSQDFTLI
GRPILQKDLVNVQATVIEKSLSHTRTHFKFKKRKQYRRINFQRQPTTVLRINSIEIKNLV
NQNKNAESLENVFY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5123.t1 | Hamap | MF_01363 | 50S ribosomal protein L21 [rplU]. | 71 | 176 | 16.11561 |
| 2 | g5123.t1 | PANTHER | PTHR21349 | 50S RIBOSOMAL PROTEIN L21 | 53 | 185 | 0.00000 |
| 3 | g5123.t1 | PANTHER | PTHR21349:SF0 | 39S RIBOSOMAL PROTEIN L21, MITOCHONDRIAL | 53 | 185 | 0.00000 |
| 1 | g5123.t1 | Pfam | PF00829 | Ribosomal prokaryotic L21 protein | 72 | 174 | 0.00000 |
| 5 | g5123.t1 | SUPERFAMILY | SSF141091 | L21p-like | 71 | 175 | 0.00000 |
| 6 | g5123.t1 | TIGRFAM | TIGR00061 | L21: ribosomal protein bL21 | 72 | 174 | 0.00000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5123/g5123.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5123.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005840 | ribosome | CC |
| GO:0003723 | RNA binding | MF |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02888 (large subunit ribosomal protein L21)
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.
