General information for g10182.t18
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pre-mRNA-splicing factor 38B.
Parent gene
- The parent gene g10182 is located on chr_1: 8139342..8139870 (+ 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 | g10182 | g10182.t18 | TSS | g10182.t18 | 8137442 | 8137442 |
| chr_1 | g10182 | g10182.t18 | isoform | g10182.t18 | 8138263 | 8139870 |
| chr_1 | g10182 | g10182.t18 | exon | g10182.t18.exon1 | 8138263 | 8139259 |
| chr_1 | g10182 | g10182.t18 | cds | g10182.t18.CDS1 | 8139258 | 8139259 |
| chr_1 | g10182 | g10182.t18 | exon | g10182.t18.exon2 | 8139327 | 8139870 |
| chr_1 | g10182 | g10182.t18 | cds | g10182.t18.CDS2 | 8139327 | 8139870 |
| chr_1 | g10182 | g10182.t18 | TTS | g10182.t18 | 8140068 | 8140068 |
Sequences
>g10182.t18 Gene=g10182 Length=1541
ATGGCGGATGAACAAGGTTTTTTATTAATTTTTTTATTTTTCACAAACGTTTAAAAATGC
CTAACAAATTTTCAATTGCTTTATTATTTATATTATTTAGAATATAGTGGAGGAAAAAAG
AAAAATAATAGTTTACCTATCTATGGAAATCATGAAACGATGAATCTTAATAACTTAATT
TTAACAAATATTCAATCAAGTGTTTATTTCAAAGGTAAGCTTCTATTCAATTCTAGCATT
CTAAAATAAACTTCATATTCCATCTTTTTTCTTATTTTTCTCCCTATTCCATCTATTTAG
GTATGTGTCAGTAGGTATGAAAAACATCTTTTAAATCTTAGACTTTGTTGCGAATTATGA
TCCCAACATTGTCTTTTAATTTTTTATAATTTGCAATAGTCACACAAAAATTATCACAAT
TTCTTTCTTCATTTTAGTGACATTATTTCAGCTGAAAACGTATCATGAAGTCATTGATGA
AATCTACTATCAAGTAAAACATCTTGAGCCTTGGGAACTTAATTCCCGGTATATATATTT
ATTTGATCAATTAACTAAAACTCATTAACAAACATTAAATATTTTTTTCAGAAAAACTCA
AGGAAATTCAGGAATGTGCGGGTAAGAGTATAGTTTATTCCTCATTAATTTACTGTAACG
CTCGATTTGCTATTTTGCGTGTTAACAATTTATGACATGCAATCCTTGCGTCAACAATTT
TCTTATTTCATTTTATGATTTTTCTTTTTTATTTTAATTAGGAGCGTAAGGGGAGTGGGC
TCGGGTGGAATAGTTAGTAGTGCAGTAAGTATAATTCATCAAAGTCACATTAACATATAG
AAGAGCTTTTTTTGCTAGAATAATATATCTCATTGTAATTTTTTTTCTTATAGTTTTGTC
TTTTATACAAACTATATACACTGAAATTGACACGAAAACAGCTAAATGGTTTAATAAAGC
ATACAGATTCGCCATATATCCGTGCTTTAGGATTCATGTATATTCGCTACACTCAACCTC
CTGCTGATTTATTTGGATGGTATGAGGAGTTTCTTCAAGATGAAGAAGAGATTGATATTA
AAGCTGGTGGAGGCCATATTTTGACAATAGGTCAAATGTGTAGACAATTCCTTGTAAAGC
TCGATTGGTTTAGTACACTCTTTCCACGAATTCCTGTTCCAATACAAAAAAGTATAGAAC
AGCGATTAAATGACTATGACAAACAAAATGGAATTGTAGCTCAACCAATTGTTTCCATCC
CACAACAACCAGAACGACGTGAACGCTCTTCAAAAGAGTATTACAGAAGTGAAAGGAGAC
GTTCTCGATCACCGATAGCGAAGCGTTCACGATCACCAACAGAAAGGCGTTATAGAGGTG
ACTTTGATGATGACGCAAGACATTCAAGACGATCACATAGCCGAGAGAAATATTCATCAA
GTAAGTCTTCAAAGTATTATAGAGATCGTTCAAGATCTCGTTCTAGAGAACGTAATGATC
GAAGAAGATACGAAGAATCGAGAAGTTCACGTCGTTATTAA
>g10182.t18 Gene=g10182 Length=181
MYIRYTQPPADLFGWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPRIP
VPIQKSIEQRLNDYDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRSRS
PTERRYRGDFDDDARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSSRR
Y
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10182.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 181 | - |
| 5 | g10182.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 93 | 109 | - |
| 6 | g10182.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 116 | 181 | - |
| 2 | g10182.t18 | PANTHER | PTHR23142 | UNCHARACTERIZED | 1 | 180 | 3.2E-37 |
| 3 | g10182.t18 | PANTHER | PTHR23142:SF2 | PRE-MRNA-SPLICING FACTOR 38B | 1 | 180 | 3.2E-37 |
| 1 | g10182.t18 | Pfam | PF03371 | PRP38 family | 1 | 67 | 3.2E-13 |
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 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.
