General information for g10182.t17
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.t17 | TSS | g10182.t17 | 8137442 | 8137442 |
| chr_1 | g10182 | g10182.t17 | isoform | g10182.t17 | 8138263 | 8139870 |
| chr_1 | g10182 | g10182.t17 | exon | g10182.t17.exon1 | 8138263 | 8138576 |
| chr_1 | g10182 | g10182.t17 | exon | g10182.t17.exon2 | 8138700 | 8138790 |
| chr_1 | g10182 | g10182.t17 | exon | g10182.t17.exon3 | 8138854 | 8138883 |
| chr_1 | g10182 | g10182.t17 | cds | g10182.t17.CDS1 | 8138876 | 8138883 |
| chr_1 | g10182 | g10182.t17 | exon | g10182.t17.exon4 | 8139024 | 8139066 |
| chr_1 | g10182 | g10182.t17 | cds | g10182.t17.CDS2 | 8139024 | 8139066 |
| chr_1 | g10182 | g10182.t17 | exon | g10182.t17.exon5 | 8139156 | 8139259 |
| chr_1 | g10182 | g10182.t17 | cds | g10182.t17.CDS3 | 8139156 | 8139259 |
| chr_1 | g10182 | g10182.t17 | exon | g10182.t17.exon6 | 8139327 | 8139870 |
| chr_1 | g10182 | g10182.t17 | cds | g10182.t17.CDS4 | 8139327 | 8139870 |
| chr_1 | g10182 | g10182.t17 | TTS | g10182.t17 | 8140068 | 8140068 |
Sequences
>g10182.t17 Gene=g10182 Length=1126
ATGGCGGATGAACAAGGTTTTTTATTAATTTTTTTATTTTTCACAAACGTTTAAAAATGC
CTAACAAATTTTCAATTGCTTTATTATTTATATTATTTAGAATATAGTGGAGGAAAAAAG
AAAAATAATAGTTTACCTATCTATGGAAATCATGAAACGATGAATCTTAATAACTTAATT
TTAACAAATATTCAATCAAGTGTTTATTTCAAAGGTAAGCTTCTATTCAATTCTAGCATT
CTAAAATAAACTTCATATTCCATCTTTTTTCTTATTTTTCTCCCTATTCCATCTATTTAG
GTATGTGTCAGTAGTGACATTATTTCAGCTGAAAACGTATCATGAAGTCATTGATGAAAT
CTACTATCAAGTAAAACATCTTGAGCCTTGGGAACTTAATTCCCGAAAAACTCAAGGAAA
TTCAGGAATGTGCGGGAGCGTAAGGGGAGTGGGCTCGGGTGGAATAGTTAGTAGTGCATT
TTGTCTTTTATACAAACTATATACACTGAAATTGACACGAAAACAGCTAAATGGTTTAAT
AAAGCATACAGATTCGCCATATATCCGTGCTTTAGGATTCATGTATATTCGCTACACTCA
ACCTCCTGCTGATTTATTTGGATGGTATGAGGAGTTTCTTCAAGATGAAGAAGAGATTGA
TATTAAAGCTGGTGGAGGCCATATTTTGACAATAGGTCAAATGTGTAGACAATTCCTTGT
AAAGCTCGATTGGTTTAGTACACTCTTTCCACGAATTCCTGTTCCAATACAAAAAAGTAT
AGAACAGCGATTAAATGACTATGACAAACAAAATGGAATTGTAGCTCAACCAATTGTTTC
CATCCCACAACAACCAGAACGACGTGAACGCTCTTCAAAAGAGTATTACAGAAGTGAAAG
GAGACGTTCTCGATCACCGATAGCGAAGCGTTCACGATCACCAACAGAAAGGCGTTATAG
AGGTGACTTTGATGATGACGCAAGACATTCAAGACGATCACATAGCCGAGAGAAATATTC
ATCAAGTAAGTCTTCAAAGTATTATAGAGATCGTTCAAGATCTCGTTCTAGAGAACGTAA
TGATCGAAGAAGATACGAAGAATCGAGAAGTTCACGTCGTTATTAA
>g10182.t17 Gene=g10182 Length=232
MCGSVRGVGSGGIVSSAFCLLYKLYTLKLTRKQLNGLIKHTDSPYIRALGFMYIRYTQPP
ADLFGWYEEFLQDEEEIDIKAGGGHILTIGQMCRQFLVKLDWFSTLFPRIPVPIQKSIEQ
RLNDYDKQNGIVAQPIVSIPQQPERRERSSKEYYRSERRRSRSPIAKRSRSPTERRYRGD
FDDDARHSRRSHSREKYSSSKSSKYYRDRSRSRSRERNDRRRYEESRSSRRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10182.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 140 | 232 | - |
| 4 | g10182.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 144 | 160 | - |
| 5 | g10182.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 167 | 232 | - |
| 2 | g10182.t17 | PANTHER | PTHR23142 | UNCHARACTERIZED | 9 | 231 | 1.8E-69 |
| 3 | g10182.t17 | PANTHER | PTHR23142:SF2 | PRE-MRNA-SPLICING FACTOR 38B | 9 | 231 | 1.8E-69 |
| 1 | g10182.t17 | Pfam | PF03371 | PRP38 family | 8 | 118 | 1.4E-33 |
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.
