General information for g11507.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Maternal protein pumilio.
Parent gene
- The parent gene g11507 is located on chr_1: 16701616..16702486 (+ 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 | g11507 | g11507.t3 | isoform | g11507.t3 | 16695283 | 16702486 |
| chr_1 | g11507 | g11507.t3 | exon | g11507.t3.exon1 | 16695283 | 16695432 |
| chr_1 | g11507 | g11507.t3 | cds | g11507.t3.CDS1 | 16695283 | 16695432 |
| chr_1 | g11507 | g11507.t3 | exon | g11507.t3.exon2 | 16698729 | 16699031 |
| chr_1 | g11507 | g11507.t3 | cds | g11507.t3.CDS2 | 16698729 | 16699031 |
| chr_1 | g11507 | g11507.t3 | exon | g11507.t3.exon3 | 16699943 | 16700165 |
| chr_1 | g11507 | g11507.t3 | cds | g11507.t3.CDS3 | 16699943 | 16700165 |
| chr_1 | g11507 | g11507.t3 | exon | g11507.t3.exon4 | 16700710 | 16701552 |
| chr_1 | g11507 | g11507.t3 | cds | g11507.t3.CDS4 | 16700710 | 16701552 |
| chr_1 | g11507 | g11507.t3 | exon | g11507.t3.exon5 | 16701616 | 16701876 |
| chr_1 | g11507 | g11507.t3 | cds | g11507.t3.CDS5 | 16701616 | 16701876 |
| chr_1 | g11507 | g11507.t3 | exon | g11507.t3.exon6 | 16701952 | 16702120 |
| chr_1 | g11507 | g11507.t3 | cds | g11507.t3.CDS6 | 16701952 | 16702120 |
| chr_1 | g11507 | g11507.t3 | exon | g11507.t3.exon7 | 16702180 | 16702486 |
| chr_1 | g11507 | g11507.t3 | cds | g11507.t3.CDS7 | 16702180 | 16702486 |
| chr_1 | g11507 | g11507.t3 | TTS | g11507.t3 | 16702556 | 16702556 |
| chr_1 | g11507 | g11507.t3 | TSS | g11507.t3 | NA | NA |
Sequences
>g11507.t3 Gene=g11507 Length=2256
ATGGTTGTCCTAGAAGGAACACAAATGACCACATCGATTGGAACGCCTTATGCACAAGGT
GCTCCAGCCTTAAAAATAGTACAAAAACGTTTTTTGGGTCTACATCAATGGCTCTCACCA
GTTTATAGCAAAGAAATTAAGGAACAACTTCAATTATTGAGATCTCAAAATCCTACTTTA
ACAAATACTCCCAATGGACAGCATATGCCTCAACCTATGCCTATGGCAACTCAACAGCAA
TTTTTGGCTCAGCAAAACGCCGCATATGCTGCTCAACAAGCTGCATCCTATATGATGCCA
GGTCAAGATGGAAATCCTTTTATGGCTACAATGCTTGCTCCCTCGTATTACGGTGTTCCA
CCTCCGCCTTGGGTTTATCCGGCTGGTCTTATTCCACAACAAGGAACTCAACCAAGACGA
CCTCTCACACCATCACAGGAAAATCAACCTTTCGTTTTACAACCTACGTTCTATGATCAA
AATGGATGTGCAATTAATATGATGTCACATCGAACTGGTACACCTATGAGATTAGTGAGC
CCAGCACCAGTAGCTGCGCCAGTTTTAGCTGTTCCTGGCACTGCAGCGCCACCTCGACCA
CCTCAAATCTATCAGCCTACCCAACAAGGCACACCACAAGCTATATACTCGCAACAAAAC
AATAGCAATGTTGGAGGTTTACAACTAAACACTGGCTTAACAACGCGTCGTGATTCTTTT
GATCGCAATACATCAGCATTTAGTCCCTCATTAGACTATAATGCAGCTGCTGCAGGAAGT
TCAGTAAGAAAATGGCCAACAACATTCAATGGTTCGTCACCAATTGGAGCACCTTTGACA
CCACCACCTTTAAGTCGAGCACCAGGTGCAGAAACAAAATATAGAAATATTGGAGGGCAA
TTACCAATGGGATTATCTGCCAGCGCTGCTTCAACTGCAGCTGCTTCGAATGCAATGTTT
GGATCTAGTAACTCTTTATTCTCGAAATTAAGCAGCGGAGCAATTCGAAGCTCTCAAAAC
ACGGGAAATAATGCAATTTCAGTAATATCTGGTGGACCAGGAGTTGCTGTAAGTGGAACT
GTGGCTACTGCTGCTGCTGCTGATAGTAAAGGACGTTCTCGATTGTTAGAAGAATTTCGT
AATCAACGCTATCCGAATCTGCAACTACGCGATCTCGCAAATCATATTGTTGAGTTTTCA
CAAGATCAACACGGATCTCGCTTTATACAACAAAAGTTGGAAAGAGCAACTGCTTCCGAA
AAGCAAATGGTGTTTAATGAAATTGTAAACTCAGCATATAGTTTGATGACTGATGTGTTT
GGAAATTATGTTATACAAAAGTTTTTTGAATATGGCACGCAAGAACAACGTGCTGCTTTA
GCATCACAAGTCAAAGGTAATGTGTTAAACCTCGCTCTTCAAATGTATGGTTGTAGAGTT
ATCCAGAAAGCACTCGAGAGTATTCCAAGTGAACAACAACAAGACATTGTGCGTGAGCTA
GAAGGACATGTATTAAAATGTGTAAAAGATCAAAACGGAAATCATGTCGTTCAGAAATGT
ATTGAGTGCGTAGATTCAACTGCATTACAATTTATTATAAATGCATTCAACGGACAAATT
TTCACTTTAAGTACTCATCCATATGGATGCAGAGTTATTCAAAGAATTTTGGAGCATTGT
TCACCCGAACAAACAGCACCAATTTTACAGGAATTACATTTGAACACTGAAAAGCTTATT
CAGGATCAATATGGAAATTATGTCATTCAGCATGTACTAGAACACGGTAAAGCTGAAGAT
AAATCTGCAATCATTAAAGCAGTTCTTGGAAAAGTATTGACGCTCTCACAGCATAAATTT
GCATCAAATGTTGTTGAAAAATGTGTTACGCATGCTACAAGAGCTGAACGTAACATGTTA
ATTGATGAAGTTTGCATGTTCAATGATACTGGACTTCAAGTGATGATGAAGGATCAATAT
GCCAATTACGTCGTTCAAAAAATGATTGATGTATCAGAACCAACTCAAAGAAAGACGCTT
TTGCACAAGATTCGACCACACATGAATTCCTTACGCAAGTACACTTATGGCAAGCATATT
ATTGCAAAGTTGGAAAAATTCTCTTTAAAATCTGGTGTAGCTTCTGTAACAACTTCTTCT
ACAGCTACCACTAATCCTAACACGTCGTCTACAACAGCTACTGATACTGTTACTTCTTCG
ACATCATCGTCGTCTTTTGGAGCAAACGGTTTATAA
>g11507.t3 Gene=g11507 Length=751
MVVLEGTQMTTSIGTPYAQGAPALKIVQKRFLGLHQWLSPVYSKEIKEQLQLLRSQNPTL
TNTPNGQHMPQPMPMATQQQFLAQQNAAYAAQQAASYMMPGQDGNPFMATMLAPSYYGVP
PPPWVYPAGLIPQQGTQPRRPLTPSQENQPFVLQPTFYDQNGCAINMMSHRTGTPMRLVS
PAPVAAPVLAVPGTAAPPRPPQIYQPTQQGTPQAIYSQQNNSNVGGLQLNTGLTTRRDSF
DRNTSAFSPSLDYNAAAAGSSVRKWPTTFNGSSPIGAPLTPPPLSRAPGAETKYRNIGGQ
LPMGLSASAASTAAASNAMFGSSNSLFSKLSSGAIRSSQNTGNNAISVISGGPGVAVSGT
VATAAAADSKGRSRLLEEFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATASE
KQMVFNEIVNSAYSLMTDVFGNYVIQKFFEYGTQEQRAALASQVKGNVLNLALQMYGCRV
IQKALESIPSEQQQDIVRELEGHVLKCVKDQNGNHVVQKCIECVDSTALQFIINAFNGQI
FTLSTHPYGCRVIQRILEHCSPEQTAPILQELHLNTEKLIQDQYGNYVIQHVLEHGKAED
KSAIIKAVLGKVLTLSQHKFASNVVEKCVTHATRAERNMLIDEVCMFNDTGLQVMMKDQY
ANYVVQKMIDVSEPTQRKTLLHKIRPHMNSLRKYTYGKHIIAKLEKFSLKSGVASVTTSS
TATTNPNTSSTTATDTVTSSTSSSSFGANGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g11507.t3 | CDD | cd07920 | Pumilio | 386 | 704 | 0.0 |
| 12 | g11507.t3 | Gene3D | G3DSA:1.25.10.10 | - | 370 | 714 | 5.8E-150 |
| 22 | g11507.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 718 | 751 | - |
| 9 | g11507.t3 | PANTHER | PTHR12537 | RNA BINDING PROTEIN PUMILIO-RELATED | 367 | 717 | 6.4E-213 |
| 10 | g11507.t3 | PANTHER | PTHR12537:SF52 | PUMILIO HOMOLOG 2 | 367 | 717 | 6.4E-213 |
| 2 | g11507.t3 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 395 | 428 | 7.7E-12 |
| 4 | g11507.t3 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 433 | 462 | 2.8E-8 |
| 8 | g11507.t3 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 467 | 500 | 1.2E-10 |
| 6 | g11507.t3 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 503 | 534 | 7.8E-6 |
| 3 | g11507.t3 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 539 | 573 | 2.3E-16 |
| 7 | g11507.t3 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 579 | 609 | 3.7E-8 |
| 5 | g11507.t3 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 612 | 645 | 8.8E-9 |
| 1 | g11507.t3 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 655 | 684 | 1.4E-6 |
| 32 | g11507.t3 | ProSiteProfiles | PS50303 | Pumilio homology domain (PUM-HD) profile. | 371 | 708 | 136.717 |
| 24 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 391 | 426 | 11.044 |
| 30 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 427 | 462 | 10.81 |
| 31 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 463 | 498 | 11.3 |
| 29 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 499 | 534 | 10.204 |
| 26 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 535 | 570 | 10.88 |
| 25 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 571 | 606 | 11.207 |
| 23 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 607 | 642 | 9.574 |
| 27 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 646 | 682 | 9.154 |
| 28 | g11507.t3 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 683 | 718 | 4.558 |
| 15 | g11507.t3 | SMART | SM00025 | pum_5 | 391 | 426 | 1.4E-6 |
| 19 | g11507.t3 | SMART | SM00025 | pum_5 | 427 | 462 | 1.9E-6 |
| 21 | g11507.t3 | SMART | SM00025 | pum_5 | 463 | 498 | 4.7E-7 |
| 18 | g11507.t3 | SMART | SM00025 | pum_5 | 499 | 534 | 1.7E-8 |
| 17 | g11507.t3 | SMART | SM00025 | pum_5 | 535 | 570 | 6.4E-9 |
| 16 | g11507.t3 | SMART | SM00025 | pum_5 | 571 | 606 | 5.3E-8 |
| 14 | g11507.t3 | SMART | SM00025 | pum_5 | 607 | 642 | 5.7E-7 |
| 20 | g11507.t3 | SMART | SM00025 | pum_5 | 647 | 682 | 1.7E-6 |
| 11 | g11507.t3 | SUPERFAMILY | SSF48371 | ARM repeat | 372 | 705 | 4.03E-120 |
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:0003723 | RNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K17943 (pumilio RNA-binding family)
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.
