General information for g6229.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Splicing factor 45.
Parent gene
- The parent gene g6229 is located on chr_2: 15425763..15426662 (+ 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_2 | g6229 | g6229.t1 | TSS | g6229.t1 | 15424518 | 15424518 |
| chr_2 | g6229 | g6229.t1 | isoform | g6229.t1 | 15424602 | 15425763 |
| chr_2 | g6229 | g6229.t1 | exon | g6229.t1.exon1 | 15424602 | 15424715 |
| chr_2 | g6229 | g6229.t1 | cds | g6229.t1.CDS1 | 15424602 | 15424715 |
| chr_2 | g6229 | g6229.t1 | exon | g6229.t1.exon2 | 15424777 | 15425763 |
| chr_2 | g6229 | g6229.t1 | cds | g6229.t1.CDS2 | 15424777 | 15425763 |
| chr_2 | g6229 | g6229.t1 | TTS | g6229.t1 | 15425785 | 15425785 |
Sequences
>g6229.t1 Gene=g6229 Length=1101
ATGTCTCTATACGATGATGTTGATACACAAACAGTTTCAGAATGGAGCTCTGGAATTAAA
TTCATGCCACAACCAACATTAAATAAGATTCAAACAAAAAATACTCGACCGAATCTTCTA
ACACCAGTTGCAAGCTTGAAACCGAAAGTAATTGATGAAAATAAACCTAAAGAAGTCATT
GTGAAGCCGAAAATCATTCAAAGTCAACCACTTCAGCCTGTAGTTGTTCAACCTAAAATA
ATAAGCCATACAAATAATGAATGGGATGATTTCTTATCAATTCAAGATGAATATAATCCT
GCAATTCCAAATGAATATGAGAAAATTGTAAAAGAAAGGCGAGAAAGAAACAAAAAGGAT
GATCGAAAAAGACATCGATCACCATCGCCAAGAAAAAGTTTCAACAGACGAAATTCAGAT
GATGAAGATTTCAGACCGACACTTGGTGGTTCTCGAAACAGTGGAACAGCAATTGCTCCA
CCAAAATCATTACAAGAAAGCTCTCCAATTATCGATATTCCAAACATTACTCAGTATGGA
GCATCAACTATTGCTGGAAGAATTATGGCAAAATACGGTTTTAAAGATGGACAAGGATTA
GGCAAGCAAGAACAAGGAATTAGCAGTGCATTACAAGTTGAAAAAACTTCAAAACGCGGG
GGTCGAATAATTAGTGAAAAAGAAGTCAAAGAGATGTCAACAATAACACAAACTCCACAA
CAGCAACAAGCACAACCAGAGCCACAAACTTCTCAAAATCCTTCTCTACCAAGTGAACAG
AGCATCACAGAAATGATGAAGAATCCAAGCAAAGTAATTTTACTCAGAAATATGGTTGGT
CCTGGTGAAGTCGATGATGATTTAGAACCTGAAGTAAAAGACGAATGCACTACAAAATAT
GGAGAAGTTGTCACTGTTCATATCATGGAAATGCCTAATCAAATACCAGAAGAAACAGTA
AGAATTTTTGTAGAATTCAGTCGAATTGAAAGCGCAATCAAAGCATTAGTTGATTTAAAT
GGAAGATTTTTTGGAGGACGTCAAGTAAGATGTCGATTTTATTCATCTGAAAAATATGAA
AACTTTATATTTAATGAATAA
>g6229.t1 Gene=g6229 Length=366
MSLYDDVDTQTVSEWSSGIKFMPQPTLNKIQTKNTRPNLLTPVASLKPKVIDENKPKEVI
VKPKIIQSQPLQPVVVQPKIISHTNNEWDDFLSIQDEYNPAIPNEYEKIVKERRERNKKD
DRKRHRSPSPRKSFNRRNSDDEDFRPTLGGSRNSGTAIAPPKSLQESSPIIDIPNITQYG
ASTIAGRIMAKYGFKDGQGLGKQEQGISSALQVEKTSKRGGRIISEKEVKEMSTITQTPQ
QQQAQPEPQTSQNPSLPSEQSITEMMKNPSKVILLRNMVGPGEVDDDLEPEVKDECTTKY
GEVVTVHIMEMPNQIPEETVRIFVEFSRIESAIKALVDLNGRFFGGRQVRCRFYSSEKYE
NFIFNE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6229.t1 | CDD | cd12647 | RRM_UHM_SPF45 | 269 | 362 | 1.22667E-51 |
| 5 | g6229.t1 | Gene3D | G3DSA:3.30.70.330 | - | 267 | 364 | 9.8E-27 |
| 14 | g6229.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 166 | - |
| 15 | g6229.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 132 | - |
| 13 | g6229.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 133 | 147 | - |
| 16 | g6229.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 149 | 166 | - |
| 17 | g6229.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 211 | 260 | - |
| 12 | g6229.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 230 | 260 | - |
| 3 | g6229.t1 | PANTHER | PTHR13288 | SPLICING FACTOR 45 SPF45 | 13 | 365 | 7.0E-87 |
| 7 | g6229.t1 | PIRSF | PIRSF031066 | SPF45 | 1 | 136 | 1.6E-8 |
| 6 | g6229.t1 | PIRSF | PIRSF031066 | SPF45 | 114 | 366 | 5.2E-90 |
| 1 | g6229.t1 | Pfam | PF01585 | G-patch domain | 182 | 221 | 3.0E-12 |
| 2 | g6229.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 299 | 350 | 5.3E-5 |
| 19 | g6229.t1 | ProSiteProfiles | PS50174 | G-patch domain profile. | 181 | 227 | 12.886 |
| 18 | g6229.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 271 | 356 | 10.548 |
| 10 | g6229.t1 | SMART | SM00443 | G-patch_5 | 179 | 225 | 3.0E-11 |
| 9 | g6229.t1 | SMART | SM00361 | rrm2_1 | 272 | 352 | 4.9E-18 |
| 11 | g6229.t1 | SMART | SM00360 | rrm1_1 | 272 | 352 | 4.9E-5 |
| 4 | g6229.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 274 | 358 | 8.28E-16 |
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:0043484 | regulation of RNA splicing | BP |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12840 (splicing factor 45)
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.
