General information for g13449.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein sarah.
Parent gene
- The parent gene g13449 is located on chr_1: 30213283..30213888 (+ 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 | g13449 | g13449.t1 | TSS | g13449.t1 | 30213124 | 30213124 |
| chr_1 | g13449 | g13449.t1 | isoform | g13449.t1 | 30213283 | 30213888 |
| chr_1 | g13449 | g13449.t1 | exon | g13449.t1.exon1 | 30213283 | 30213888 |
| chr_1 | g13449 | g13449.t1 | cds | g13449.t1.CDS1 | 30213283 | 30213888 |
| chr_1 | g13449 | g13449.t1 | TTS | g13449.t1 | 30214148 | 30214148 |
Sequences
>g13449.t1 Gene=g13449 Length=606
ATGGAGGATGAAAATAATTTTAAAAATGACCATTTATTAAATTCTGAGGAATCAGATCAA
GAAGAAACATCACTAGTTGTCTCGAATATAAATTCTGAAGTATTTAGTTCGCCTGAACTA
AAAGAAGAAATTGAAAATCTCTTTCGAGAATTCTCAGAAGAAATTACATTCCAATATTTC
AAATCATTTCATCGACTGAGAGTAAATTTTGCTAATTCAGAACCAGCTGCTGAAGCGTGT
GCAAAAATTCATTTGCGAGAATTTCACAATTCAGTGTTAAAATGTCATTTTATACGACCA
ATTATATTGAATAAGAAATCAAACAAGAGCCTAGAACTACCAAAGCCAACAAAACAATTT
CTCATTAGTCCACCATCCTCACCTCCGTTAGGATGGGAACAAATTGAAGAATCTGAACCA
ATTTTTAATCATGAATTAGTAGCTGCTTTATCAAACTTAACATCTGGTGGTGAAATTCAT
GAAATTCATGCAGCATCTGAAAATCAACCAGCAATTTATGTTCATACAGCAATTGATCAA
AGACAAAGACCAAAATTAGAATTTGTTCAAACAAGATGTCCAGAAAGAAAATCGAATAAT
CTATGA
>g13449.t1 Gene=g13449 Length=201
MEDENNFKNDHLLNSEESDQEETSLVVSNINSEVFSSPELKEEIENLFREFSEEITFQYF
KSFHRLRVNFANSEPAAEACAKIHLREFHNSVLKCHFIRPIILNKKSNKSLELPKPTKQF
LISPPSSPPLGWEQIEESEPIFNHELVAALSNLTSGGEIHEIHAASENQPAIYVHTAIDQ
RQRPKLEFVQTRCPERKSNNL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13449.t1 | CDD | cd12434 | RRM_RCAN_like | 25 | 97 | 1.80732E-22 |
| 6 | g13449.t1 | Gene3D | G3DSA:3.30.70.330 | - | 19 | 122 | 3.0E-30 |
| 4 | g13449.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 24 | - |
| 5 | g13449.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 2 | g13449.t1 | PANTHER | PTHR10300 | CALCIPRESSIN | 9 | 198 | 1.1E-53 |
| 1 | g13449.t1 | Pfam | PF04847 | Calcipressin | 34 | 174 | 2.7E-30 |
| 3 | g13449.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 20 | 124 | 3.52E-19 |
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:0019722 | calcium-mediated signaling | BP |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K17901 (calcipressin-1)
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.
