General information for g1921.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 39S ribosomal protein L1, mitochondrial.
Parent gene
- The parent gene g1921 is located on chr_3: 13865011..13865896 (+ 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 | g1921 | g1921.t1 | TSS | g1921.t1 | 13864724 | 13864724 |
| chr_3 | g1921 | g1921.t1 | isoform | g1921.t1 | 13864753 | 13865896 |
| chr_3 | g1921 | g1921.t1 | exon | g1921.t1.exon1 | 13864753 | 13864943 |
| chr_3 | g1921 | g1921.t1 | cds | g1921.t1.CDS1 | 13864753 | 13864943 |
| chr_3 | g1921 | g1921.t1 | exon | g1921.t1.exon2 | 13864999 | 13865896 |
| chr_3 | g1921 | g1921.t1 | cds | g1921.t1.CDS2 | 13864999 | 13865896 |
| chr_3 | g1921 | g1921.t1 | TTS | g1921.t1 | 13866060 | 13866060 |
Sequences
>g1921.t1 Gene=g1921 Length=1089
ATGCTTCGAAAATTACCGAGTCTTTTTAATAATATTTTAAGCGTAAATCAAGTTCGACAG
AATGCAAGACCGCTATTTATTAGTGCAACTAATGAAGCTGCACGTAAAGGAACACGTGAG
AAAGCAAGAAAAAAGAAGGTAAAGGTAGAAATCAAAAAAGTCGGTTTTATTCCACACAAT
CTTAGGAAGAAAGTGAGAGTAACAGTTAATAAACACCAAGATGATTCATGGAAACAAATT
CCACAAGATGATGTATATATTCAAAAATATTATCAATATAGAACTTTCACAGTTGAAGAT
GCAATCAAATGTCATCAAGAAACTCATCATCCAACGATGTATAATGTTCCAAATGCACCA
ATTTTAGCTGAAATTGAAATAAACATGCAAGGCGAAAAGATTACAAGATTCGTAGATAAC
TTTCATCGAATGGCTCCGATAAATTATAAATTTAATCATGGCGAAGAAAGAACAGTTCTC
GCCTTTGCTAAAGGACAAGAATACATTGATATAGCTAAAAAAGCTGGTGCAACGCTCGCT
GGAGACGGAGGTTTAGTTAAAAGTATTCAAAATGGCGATTTATCTTTCAATGATTTTCAA
TTTATTGTTGCGCATTCAAATATTCTTCACGAAATTATGCCTATTAGAGGTTTACTAAAA
AGGCGATTTCCAAATCCTAAAAATGGAACATTAGGTACTGATTTAGAAGAAATGGTTCAA
AAGTTTCTTAATGGAATCACATATAGTGTAAAGAAAGATGAGAATCAACAAAATTTTGCA
AATCTTACCGCTCAGTTTGGTACTCTCGATATGGATGTAAAGCATTTAGAAGATAATTTA
GCATCATTGCTACAAGACATTAATAAAATGCGTCCAAAACGTGAAGGAAAATTTATTACA
AGAGTTTACATTAACAGTCCACCATCATCAGAAAAATTGAAAATTAATCCCTTCGTGTAC
GTGCCAGAAGAGCAAACCTTTGCAAAAAAGAAAACGTCAGCGAAAGTTGCAGAAGAGGAA
GACGAAGATGAAGCGACAGCAGCAGAAGACGAGGAAGAAGTAAAAGAAAAAAAGGAAGCT
GTTAATTAA
>g1921.t1 Gene=g1921 Length=362
MLRKLPSLFNNILSVNQVRQNARPLFISATNEAARKGTREKARKKKVKVEIKKVGFIPHN
LRKKVRVTVNKHQDDSWKQIPQDDVYIQKYYQYRTFTVEDAIKCHQETHHPTMYNVPNAP
ILAEIEINMQGEKITRFVDNFHRMAPINYKFNHGEERTVLAFAKGQEYIDIAKKAGATLA
GDGGLVKSIQNGDLSFNDFQFIVAHSNILHEIMPIRGLLKRRFPNPKNGTLGTDLEEMVQ
KFLNGITYSVKKDENQQNFANLTAQFGTLDMDVKHLEDNLASLLQDINKMRPKREGKFIT
RVYINSPPSSEKLKINPFVYVPEEQTFAKKKTSAKVAEEEDEDEATAAEDEEEVKEKKEA
VN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1921.t1 | CDD | cd00403 | Ribosomal_L1 | 98 | 309 | 8.23922E-27 |
| 6 | g1921.t1 | Gene3D | G3DSA:3.30.190.20 | - | 147 | 307 | 1.5E-26 |
| 5 | g1921.t1 | Gene3D | G3DSA:3.40.50.790 | - | 150 | 245 | 1.5E-26 |
| 4 | g1921.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 328 | 362 | - |
| 2 | g1921.t1 | PANTHER | PTHR36427 | 54S RIBOSOMAL PROTEIN L1, MITOCHONDRIAL | 15 | 310 | 2.7E-34 |
| 1 | g1921.t1 | Pfam | PF00687 | Ribosomal protein L1p/L10e family | 124 | 309 | 1.5E-12 |
| 3 | g1921.t1 | SUPERFAMILY | SSF56808 | Ribosomal protein L1 | 82 | 309 | 8.89E-31 |
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 K02863 (large subunit ribosomal protein L1)
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.
