General information for g14138.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16.
Parent gene
- The parent gene g14138 is located on chr_1: 34859209..34863760 (+ 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 | g14138 | g14138.t2 | isoform | g14138.t2 | 34858053 | 34859209 |
| chr_1 | g14138 | g14138.t2 | exon | g14138.t2.exon1 | 34858053 | 34859209 |
| chr_1 | g14138 | g14138.t2 | cds | g14138.t2.CDS1 | 34858055 | 34859209 |
| chr_1 | g14138 | g14138.t2 | TTS | g14138.t2 | 34859264 | 34859264 |
| chr_1 | g14138 | g14138.t2 | TSS | g14138.t2 | NA | NA |
Sequences
>g14138.t2 Gene=g14138 Length=1157
GTATGGACGCACTTCAAATTTATCCAATTTCTCAGGCAAATGCAAATCAACGTTCTGGAA
GAGCAGGCAGAACAGGTCCTGGAATGGCATATCGTTTATACACGGAGAGGCAATATAAAG
ATGAATTACTTCCTCTTACGGTTCCTGAAATTCAGAGAACAAATTTAGCCAACACAGTTC
TTTTACTCAAATCACTTGGTGTAGTTGATTTACTATCATTTCATTTTATGGATCCACCAC
CTCAAGACAATATTTTGAATTCACTCTATCAGTTATGGATTTTAGGCGCATTAGATCACA
CTGGTCGATTGGCGCCTCTTGGACGAGTTATGGCTGAATTTCCTTTAGATCCGCCACAAT
GTCAAATGCTAATCGTTTCATGTGAAATGGAATGTTCAGCAGAAGTTCTTATTATAGTAT
CAATGCTTTCGGTGCCATCAATTTTTTACAGACCAAAAGGACGCGAAGAAGAAGCAGATA
ATGTTAGAGAAAAATTTCAAGTTCCTGAATCAGATCATTTAACATATTTGAATGTATATC
AGCAATGGAAAATGAATAATTATTCTTCAAATTGGGCAAACGAGCATTTCATTCATATAA
AAGCTCTAAGAAAAGTGAGAGAAGTGAGGCAACAACTTAAAGATATTCTCATTCAACAGA
AATTGGAAGTTAAATCGTGTGGAACAAATTGGGACATTATTAGAAAATGTATTTGCTCAG
CCTATTTCTATCAGGCTGCTCGTTTAAAAGGTATTGGTGAATATGTCAATTTGAGAACAG
GCATGCCTTGTCATTTGCATCCAACTTCTGCTCTTTATGGATTGGGAACTTCACCAGAAT
ATGTCGTTTATCATGAATTGGTAATGACAGCCAAAGAATATATGCAATGTGCAACAGCTG
TTGACGGTTATTGGTTGGCTGAATTAGGTCCGATGTTTTTCTCTGTAAAAGAATCAGGAA
AAAGTGGTAGAGATAAAAGAAAGCAAGCAGCTGAACATTTGCATAAAATGGAATCACAAA
TGCAAGAAGCACAAGAAGAAATTGAAAGGGAGAAACAATTGAATGCTCAAAAGCAAGAAG
CAATAATGGCAAAGCAAGAAATTGTTACTCCAGGCACTTCAACACCTAGAAGAACTCCAG
CAAGAATTGGACTTTGA
>g14138.t2 Gene=g14138 Length=384
MDALQIYPISQANANQRSGRAGRTGPGMAYRLYTERQYKDELLPLTVPEIQRTNLANTVL
LLKSLGVVDLLSFHFMDPPPQDNILNSLYQLWILGALDHTGRLAPLGRVMAEFPLDPPQC
QMLIVSCEMECSAEVLIIVSMLSVPSIFYRPKGREEEADNVREKFQVPESDHLTYLNVYQ
QWKMNNYSSNWANEHFIHIKALRKVREVRQQLKDILIQQKLEVKSCGTNWDIIRKCICSA
YFYQAARLKGIGEYVNLRTGMPCHLHPTSALYGLGTSPEYVVYHELVMTAKEYMQCATAV
DGYWLAELGPMFFSVKESGKSGRDKRKQAAEHLHKMESQMQEAQEEIEREKQLNAQKQEA
IMAKQEIVTPGTSTPRRTPARIGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g14138.t2 | Coils | Coil | Coil | 326 | 360 | - |
| 7 | g14138.t2 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 44 | 1.9E-13 |
| 8 | g14138.t2 | Gene3D | G3DSA:1.20.120.1080 | - | 53 | 174 | 2.3E-28 |
| 3 | g14138.t2 | PANTHER | PTHR18934 | ATP-DEPENDENT RNA HELICASE | 1 | 315 | 2.7E-152 |
| 4 | g14138.t2 | PANTHER | PTHR18934:SF233 | PRE-MRNA-SPLICING FACTOR ATP-DEPENDENT RNA HELICASE PRP16 | 1 | 315 | 2.7E-152 |
| 2 | g14138.t2 | Pfam | PF04408 | Helicase associated domain (HA2) | 88 | 173 | 2.0E-19 |
| 1 | g14138.t2 | Pfam | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 233 | 310 | 2.6E-15 |
| 6 | g14138.t2 | SMART | SM00847 | ha2_5 | 86 | 176 | 3.3E-33 |
| 5 | g14138.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 2 | 249 | 1.9E-46 |
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:0004386 | helicase activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
