General information for g1138.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Poly(U)-binding-splicing factor half pint.
Parent gene
- The parent gene g1138 is located on chr_3: 8380940..8381516 (+ 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_3 | g1138 | g1138.t1 | TSS | g1138.t1 | 8376843 | 8376843 |
| chr_3 | g1138 | g1138.t1 | isoform | g1138.t1 | 8377006 | 8381516 |
| chr_3 | g1138 | g1138.t1 | exon | g1138.t1.exon1 | 8377006 | 8377008 |
| chr_3 | g1138 | g1138.t1 | cds | g1138.t1.CDS1 | 8377006 | 8377008 |
| chr_3 | g1138 | g1138.t1 | exon | g1138.t1.exon2 | 8377083 | 8377170 |
| chr_3 | g1138 | g1138.t1 | cds | g1138.t1.CDS2 | 8377083 | 8377170 |
| chr_3 | g1138 | g1138.t1 | exon | g1138.t1.exon3 | 8379578 | 8379860 |
| chr_3 | g1138 | g1138.t1 | cds | g1138.t1.CDS3 | 8379578 | 8379860 |
| chr_3 | g1138 | g1138.t1 | exon | g1138.t1.exon4 | 8380086 | 8380666 |
| chr_3 | g1138 | g1138.t1 | cds | g1138.t1.CDS4 | 8380086 | 8380666 |
| chr_3 | g1138 | g1138.t1 | exon | g1138.t1.exon5 | 8380732 | 8381346 |
| chr_3 | g1138 | g1138.t1 | cds | g1138.t1.CDS5 | 8380732 | 8381346 |
| chr_3 | g1138 | g1138.t1 | exon | g1138.t1.exon6 | 8381407 | 8381516 |
| chr_3 | g1138 | g1138.t1 | cds | g1138.t1.CDS6 | 8381407 | 8381516 |
| chr_3 | g1138 | g1138.t1 | TTS | g1138.t1 | 8381717 | 8381717 |
Sequences
>g1138.t1 Gene=g1138 Length=1680
ATGGGCAACAACAAGGATAATTTTGACACAGATTCAACTACTGGAAGTGAACACTCATCA
TCACCATCAAAAAGGATGAAAACTGATAAAGATTCATCTTCCTCCAAGCGTGATTTCAGA
AAGGAGCCAATTTACAACATTAAGCAAATAGGTGACGTTTCATTTGGTCCGGGTACCCGT
TCTGCTGTTTTTGGTGGTGGTTTACCGCAATTGAACAGTGAACAAAAGGATACTGTAAAG
AAGGCGAAAAAATATGCAATGGAACAAAGTATTAGAATGGTTCTCATGAAACAAACACTT
GCACACCAACAACAACAATTAGCAAGTCAAAGAACTCAAGTTCAAAGGCAGCAAGCACTT
GCTCTTATGTGCAGAGTCTATGTTGGGAGTATTTCATTTGAACTTAAAGAAGATACAATT
CGTGCAGCGTTTCTTCCTTTTGGTCCAATCAAATCAATCAATATGTCTTGGGATCCTGTG
ACACAAAAACATAAAGGATTTGCTTTTGTTGAATATGAGATTCCTGAAGGAGCTCAACTT
GCTTTAGAACAAATGAATGGAGCAATGTTAGGTGGAAGAAACATCAAAGTGGGAAGACCA
AGTAACATGCCTCAGGCACAACAAGTGATTGATGAAATTCAAGAGGAAGCCAAAAATTAT
AATCGTATTTACATCGCATCAATTCATCCAGAATTGACTGAAGAGGATATTAAAAGTGTA
TTCGAAGCGTTTGGTGCGATTGTTTTCTGCAAATTAGCGCAAGGCACATCACCTGGAAGT
CATAAAGGATATGGCTTTATTGAATACAATACAAACCAAGCAGCTCTCGAATCAATCGCA
AGTATGAATCTATTTGACTTGGGAGGACAATTATTAAGAGTAGGCAGGGCAATCACACCA
CCCAATGCTTTAGTTAGTCCTGCAGTAAATTCTTCAATGCCAACTGCAGCTGCTGTTGCT
GCAGCTGCAGCTACCGCAAAAATTCAAGCAATGGATGCTGTGCAAGCGAATGTTCTTGGT
GCAGCAGCTCCCACACTTGGTTTGAAAACTCTTGCAGCATCAACTCCCGCAGTAACTCTT
CCAACTCCAATTGTAACTCAAACAACAATTACTCCACCTGTCGTACTTCCCGTAGCAGCA
GTGCTTCAACAAAGTCACATCACACCAATTGGCGTCTCTACAAATTTACCTTCATTGATA
TCAAATGAAACACAACAGAATGCAGAAGAATTGGTAAAACAAAAACAAGAAGAATTACAA
AAGAAATTATTAGAAGAGGGTGAACCAACTTTACAACAACAAGAATCAATGTCCATCAAA
GGTCAAAATGCAAGACATTTAGTCATGCAAAGACTTATGAGACCACGTGAAAGTAAAGTT
GTAATTTTAAGAAATATGGTTGGACCTGAAGATGTTGATGAGACACTTCAAGAAGAAATT
CAAGATGAATGCAGTAAATATGGTGTTGTAGAGAAAGTTATTATTTATAAAGAGAAACAA
ACTGACAATGATGATGACGATTATGGTGATGTTATTGTAAAAATTTTCGTAGAATTTTCG
ATGTCATCTGAAGCTGACAAGGCAAGTTCTGGTTTAAATGGTCGATTTTTTGGAGGACGA
TTGGTTAAAGCTGAGAGCTACGACCAAGCACTTTTTGACCACAGTGACTTTTCTGGTTGA
>g1138.t1 Gene=g1138 Length=559
MGNNKDNFDTDSTTGSEHSSSPSKRMKTDKDSSSSKRDFRKEPIYNIKQIGDVSFGPGTR
SAVFGGGLPQLNSEQKDTVKKAKKYAMEQSIRMVLMKQTLAHQQQQLASQRTQVQRQQAL
ALMCRVYVGSISFELKEDTIRAAFLPFGPIKSINMSWDPVTQKHKGFAFVEYEIPEGAQL
ALEQMNGAMLGGRNIKVGRPSNMPQAQQVIDEIQEEAKNYNRIYIASIHPELTEEDIKSV
FEAFGAIVFCKLAQGTSPGSHKGYGFIEYNTNQAALESIASMNLFDLGGQLLRVGRAITP
PNALVSPAVNSSMPTAAAVAAAAATAKIQAMDAVQANVLGAAAPTLGLKTLAASTPAVTL
PTPIVTQTTITPPVVLPVAAVLQQSHITPIGVSTNLPSLISNETQQNAEELVKQKQEELQ
KKLLEEGEPTLQQQESMSIKGQNARHLVMQRLMRPRESKVVILRNMVGPEDVDETLQEEI
QDECSKYGVVEKVIIYKEKQTDNDDDDYGDVIVKIFVEFSMSSEADKASSGLNGRFFGGR
LVKAESYDQALFDHSDFSG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g1138.t1 | CDD | cd12370 | RRM1_PUF60 | 124 | 199 | 1.82516E-53 |
| 13 | g1138.t1 | CDD | cd12371 | RRM2_PUF60 | 221 | 297 | 1.03838E-44 |
| 11 | g1138.t1 | Coils | Coil | Coil | 203 | 223 | - |
| 10 | g1138.t1 | Coils | Coil | Coil | 401 | 425 | - |
| 12 | g1138.t1 | Coils | Coil | Coil | 557 | 559 | - |
| 9 | g1138.t1 | Gene3D | G3DSA:3.30.70.330 | - | 112 | 220 | 2.1E-30 |
| 8 | g1138.t1 | Gene3D | G3DSA:3.30.70.330 | - | 221 | 313 | 2.4E-17 |
| 7 | g1138.t1 | Gene3D | G3DSA:3.30.70.330 | - | 458 | 548 | 2.1E-26 |
| 22 | g1138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 23 | g1138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 41 | - |
| 21 | g1138.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 22 | 41 | - |
| 3 | g1138.t1 | PANTHER | PTHR47330 | POLY(U)-BINDING-SPLICING FACTOR PUF60-B-RELATED | 24 | 559 | 6.2E-230 |
| 4 | g1138.t1 | PANTHER | PTHR47330:SF1 | POLY(U)-BINDING-SPLICING FACTOR PUF60-B-RELATED | 24 | 559 | 6.2E-230 |
| 1 | g1138.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 126 | 196 | 2.8E-18 |
| 2 | g1138.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 223 | 292 | 8.5E-12 |
| 26 | g1138.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 124 | 202 | 17.353 |
| 27 | g1138.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 221 | 299 | 15.221 |
| 25 | g1138.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 459 | 549 | 9.729 |
| 17 | g1138.t1 | SMART | SM00361 | rrm2_1 | 125 | 198 | 0.28 |
| 20 | g1138.t1 | SMART | SM00360 | rrm1_1 | 125 | 198 | 5.2E-24 |
| 15 | g1138.t1 | SMART | SM00361 | rrm2_1 | 222 | 295 | 11.0 |
| 18 | g1138.t1 | SMART | SM00360 | rrm1_1 | 222 | 295 | 9.7E-16 |
| 16 | g1138.t1 | SMART | SM00361 | rrm2_1 | 460 | 545 | 8.6E-14 |
| 19 | g1138.t1 | SMART | SM00360 | rrm1_1 | 460 | 545 | 0.02 |
| 6 | g1138.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 103 | 203 | 3.36E-25 |
| 5 | g1138.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 220 | 545 | 3.23E-25 |
| 24 | g1138.t1 | TIGRFAM | TIGR01645 | half-pint: poly-U binding splicing factor, half-pint family | 42 | 377 | 1.2E-163 |
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:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12838 (poly(U)-binding-splicing factor PUF60)
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.
