General information for g11507.t1
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.t1 | TSS | g11507.t1 | 16688809 | 16688809 |
| chr_1 | g11507 | g11507.t1 | isoform | g11507.t1 | 16689819 | 16702486 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon1 | 16689819 | 16690001 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS1 | 16689819 | 16690001 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon2 | 16690092 | 16690502 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS2 | 16690092 | 16690502 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon3 | 16690569 | 16690786 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS3 | 16690569 | 16690786 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon4 | 16690845 | 16690968 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS4 | 16690845 | 16690968 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon5 | 16691035 | 16691144 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS5 | 16691035 | 16691144 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon6 | 16691207 | 16691444 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS6 | 16691207 | 16691444 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon7 | 16691541 | 16691633 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS7 | 16691541 | 16691633 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon8 | 16698729 | 16699031 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS8 | 16698729 | 16699031 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon9 | 16699943 | 16700165 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS9 | 16699943 | 16700165 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon10 | 16700710 | 16701552 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS10 | 16700710 | 16701552 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon11 | 16701616 | 16701876 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS11 | 16701616 | 16701876 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon12 | 16701952 | 16702120 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS12 | 16701952 | 16702120 |
| chr_1 | g11507 | g11507.t1 | exon | g11507.t1.exon13 | 16702180 | 16702486 |
| chr_1 | g11507 | g11507.t1 | cds | g11507.t1.CDS13 | 16702180 | 16702486 |
| chr_1 | g11507 | g11507.t1 | TTS | g11507.t1 | 16702556 | 16702556 |
Sequences
>g11507.t1 Gene=g11507 Length=3483
ATGAAGTTGCTAGGAGGTTCTAACGATGAAAATGCCGAATCCGGTAATCGTCCACCAATC
AGAACTTCCGATGATGCTGCAACCGCAGCTGCTGTTGCTTATGGTTTTCATCCTCAAGAA
AATGAATTTCCTCCTGCAGCATTTGTACCGAAAAGATGGGCTGGAACTGATGATTTAGTA
GAGAATCCTGAAAAATGGAAGTATTCTTCAATTTATCAACCAGCATTGCAACAACAACAA
CAGCAACCATTTAGCAGTCAAAATCAGCAAAATGCAATTAAGCCTCCTCCACCAACGATG
CTAAATCATCCTTCTCAAATTCCAAATGCAATTCAATCAAATGCTCATATGAATCCAACA
ACAATGTTAAACCAAACTATAAATATGAACAATACTAATACCTTAGCTCCTCATCATCAA
CATGGCATGCATCCTTCAATGTACGATCATATGTTGAATCCAATGAATATGAATGGGATA
CAAAAGGGTCCATCAGAATTTATATATTTGAATCAACAACATGCTGCTCCTCCACCACAT
CATAATATGAGTCAGTTGGCAGCACAAAATCAATATTTACCATCTCGTAATAACCTTGCT
TCTTCAGCAACTAAAAAATTATGGGATAACAAAAATGACATGAAAAACACTGGATCTTTA
CAATTGGCACCTTTACAGATGCCTGGTAATGAACATCAAATTTGGCCAAAAGATACACAA
GGTGTTTGGTCGAAAGAACAACAAATGTGGTCTAATCAAGATAATAGTGGTCTTATTCCG
AGAAGAAATGACGTTATGACAGGAATATTAAGTCCGCGTGATTCTACTGGTGGACTTGGA
GTTAAAATGGTTGAATATGTTCTCGGAGGATCGCCAACAAATAAGGAAAGTCCATTAGAT
GCTCGTTTGAGAAATTTAAAGATTGACGAAGTTAAGGGTAACGATGATAAAGAAAGTTCA
TCACCATTTGAAACTAACGGATTGAAAAAAGACGATTCGACTTCTAATGGGACAGCTAAT
GGTATTGATGACGATAAAGGTTTTAATCGCACTCCTGGCTCACGTCAACCATCGCCAGCA
GAGGAGCATTTAGCTAGAAATGCATTTGGTTTAGAACAAAGTATTAACGTCAATAACTTT
TCTCAACCTTTGATGCAACACATGTTGACTGGACATAATCATCATGACCAACAGCAGCAG
CAACAGCAACAACAAATGAGTTCAGCTTTTCATCCTCAACATGCAATTGGTCATCACGTT
TTGAATGGCGGAATGCCAGTTCAGAATCCAATGGTTACTCAAGGTCAAAATCATATTGAT
TCTTCAAACATGCTTCAGCAACAACAACAGCAGCAACAGCAACAACATGGTTATGAGCAA
TTATTGAGATCTCAAAATCCTACTTTAACAAATACTCCCAATGGACAGCATATGCCTCAA
CCTATGCCTATGGCAACTCAACAGCAATTTTTGGCTCAGCAAAACGCCGCATATGCTGCT
CAACAAGCTGCATCCTATATGATGCCAGGTCAAGATGGAAATCCTTTTATGGCTACAATG
CTTGCTCCCTCGTATTACGGTGTTCCACCTCCGCCTTGGGTTTATCCGGCTGGTCTTATT
CCACAACAAGGAACTCAACCAAGACGACCTCTCACACCATCACAGGAAAATCAACCTTTC
GTTTTACAACCTACGTTCTATGATCAAAATGGATGTGCAATTAATATGATGTCACATCGA
ACTGGTACACCTATGAGATTAGTGAGCCCAGCACCAGTAGCTGCGCCAGTTTTAGCTGTT
CCTGGCACTGCAGCGCCACCTCGACCACCTCAAATCTATCAGCCTACCCAACAAGGCACA
CCACAAGCTATATACTCGCAACAAAACAATAGCAATGTTGGAGGTTTACAACTAAACACT
GGCTTAACAACGCGTCGTGATTCTTTTGATCGCAATACATCAGCATTTAGTCCCTCATTA
GACTATAATGCAGCTGCTGCAGGAAGTTCAGTAAGAAAATGGCCAACAACATTCAATGGT
TCGTCACCAATTGGAGCACCTTTGACACCACCACCTTTAAGTCGAGCACCAGGTGCAGAA
ACAAAATATAGAAATATTGGAGGGCAATTACCAATGGGATTATCTGCCAGCGCTGCTTCA
ACTGCAGCTGCTTCGAATGCAATGTTTGGATCTAGTAACTCTTTATTCTCGAAATTAAGC
AGCGGAGCAATTCGAAGCTCTCAAAACACGGGAAATAATGCAATTTCAGTAATATCTGGT
GGACCAGGAGTTGCTGTAAGTGGAACTGTGGCTACTGCTGCTGCTGCTGATAGTAAAGGA
CGTTCTCGATTGTTAGAAGAATTTCGTAATCAACGCTATCCGAATCTGCAACTACGCGAT
CTCGCAAATCATATTGTTGAGTTTTCACAAGATCAACACGGATCTCGCTTTATACAACAA
AAGTTGGAAAGAGCAACTGCTTCCGAAAAGCAAATGGTGTTTAATGAAATTGTAAACTCA
GCATATAGTTTGATGACTGATGTGTTTGGAAATTATGTTATACAAAAGTTTTTTGAATAT
GGCACGCAAGAACAACGTGCTGCTTTAGCATCACAAGTCAAAGGTAATGTGTTAAACCTC
GCTCTTCAAATGTATGGTTGTAGAGTTATCCAGAAAGCACTCGAGAGTATTCCAAGTGAA
CAACAACAAGACATTGTGCGTGAGCTAGAAGGACATGTATTAAAATGTGTAAAAGATCAA
AACGGAAATCATGTCGTTCAGAAATGTATTGAGTGCGTAGATTCAACTGCATTACAATTT
ATTATAAATGCATTCAACGGACAAATTTTCACTTTAAGTACTCATCCATATGGATGCAGA
GTTATTCAAAGAATTTTGGAGCATTGTTCACCCGAACAAACAGCACCAATTTTACAGGAA
TTACATTTGAACACTGAAAAGCTTATTCAGGATCAATATGGAAATTATGTCATTCAGCAT
GTACTAGAACACGGTAAAGCTGAAGATAAATCTGCAATCATTAAAGCAGTTCTTGGAAAA
GTATTGACGCTCTCACAGCATAAATTTGCATCAAATGTTGTTGAAAAATGTGTTACGCAT
GCTACAAGAGCTGAACGTAACATGTTAATTGATGAAGTTTGCATGTTCAATGATACTGGA
CTTCAAGTGATGATGAAGGATCAATATGCCAATTACGTCGTTCAAAAAATGATTGATGTA
TCAGAACCAACTCAAAGAAAGACGCTTTTGCACAAGATTCGACCACACATGAATTCCTTA
CGCAAGTACACTTATGGCAAGCATATTATTGCAAAGTTGGAAAAATTCTCTTTAAAATCT
GGTGTAGCTTCTGTAACAACTTCTTCTACAGCTACCACTAATCCTAACACGTCGTCTACA
ACAGCTACTGATACTGTTACTTCTTCGACATCATCGTCGTCTTTTGGAGCAAACGGTTTA
TAA
>g11507.t1 Gene=g11507 Length=1160
MKLLGGSNDENAESGNRPPIRTSDDAATAAAVAYGFHPQENEFPPAAFVPKRWAGTDDLV
ENPEKWKYSSIYQPALQQQQQQPFSSQNQQNAIKPPPPTMLNHPSQIPNAIQSNAHMNPT
TMLNQTINMNNTNTLAPHHQHGMHPSMYDHMLNPMNMNGIQKGPSEFIYLNQQHAAPPPH
HNMSQLAAQNQYLPSRNNLASSATKKLWDNKNDMKNTGSLQLAPLQMPGNEHQIWPKDTQ
GVWSKEQQMWSNQDNSGLIPRRNDVMTGILSPRDSTGGLGVKMVEYVLGGSPTNKESPLD
ARLRNLKIDEVKGNDDKESSSPFETNGLKKDDSTSNGTANGIDDDKGFNRTPGSRQPSPA
EEHLARNAFGLEQSINVNNFSQPLMQHMLTGHNHHDQQQQQQQQQMSSAFHPQHAIGHHV
LNGGMPVQNPMVTQGQNHIDSSNMLQQQQQQQQQQHGYEQLLRSQNPTLTNTPNGQHMPQ
PMPMATQQQFLAQQNAAYAAQQAASYMMPGQDGNPFMATMLAPSYYGVPPPPWVYPAGLI
PQQGTQPRRPLTPSQENQPFVLQPTFYDQNGCAINMMSHRTGTPMRLVSPAPVAAPVLAV
PGTAAPPRPPQIYQPTQQGTPQAIYSQQNNSNVGGLQLNTGLTTRRDSFDRNTSAFSPSL
DYNAAAAGSSVRKWPTTFNGSSPIGAPLTPPPLSRAPGAETKYRNIGGQLPMGLSASAAS
TAAASNAMFGSSNSLFSKLSSGAIRSSQNTGNNAISVISGGPGVAVSGTVATAAAADSKG
RSRLLEEFRNQRYPNLQLRDLANHIVEFSQDQHGSRFIQQKLERATASEKQMVFNEIVNS
AYSLMTDVFGNYVIQKFFEYGTQEQRAALASQVKGNVLNLALQMYGCRVIQKALESIPSE
QQQDIVRELEGHVLKCVKDQNGNHVVQKCIECVDSTALQFIINAFNGQIFTLSTHPYGCR
VIQRILEHCSPEQTAPILQELHLNTEKLIQDQYGNYVIQHVLEHGKAEDKSAIIKAVLGK
VLTLSQHKFASNVVEKCVTHATRAERNMLIDEVCMFNDTGLQVMMKDQYANYVVQKMIDV
SEPTQRKTLLHKIRPHMNSLRKYTYGKHIIAKLEKFSLKSGVASVTTSSTATTNPNTSST
TATDTVTSSTSSSSFGANGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g11507.t1 | CDD | cd07920 | Pumilio | 795 | 1113 | 1.86444E-180 |
| 14 | g11507.t1 | Gene3D | G3DSA:1.25.10.10 | - | 779 | 1123 | 1.4E-149 |
| 27 | g11507.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 26 | g11507.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 310 | 361 | - |
| 29 | g11507.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 310 | 325 | - |
| 24 | g11507.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 326 | 342 | - |
| 28 | g11507.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 391 | 411 | - |
| 25 | g11507.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1127 | 1160 | - |
| 9 | g11507.t1 | PANTHER | PTHR12537 | RNA BINDING PROTEIN PUMILIO-RELATED | 262 | 391 | 5.8E-220 |
| 11 | g11507.t1 | PANTHER | PTHR12537:SF52 | PUMILIO HOMOLOG 2 | 262 | 391 | 5.8E-220 |
| 10 | g11507.t1 | PANTHER | PTHR12537 | RNA BINDING PROTEIN PUMILIO-RELATED | 772 | 1126 | 5.8E-220 |
| 12 | g11507.t1 | PANTHER | PTHR12537:SF52 | PUMILIO HOMOLOG 2 | 772 | 1126 | 5.8E-220 |
| 2 | g11507.t1 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 804 | 837 | 1.3E-11 |
| 5 | g11507.t1 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 842 | 871 | 4.7E-8 |
| 4 | g11507.t1 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 876 | 909 | 1.9E-10 |
| 3 | g11507.t1 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 912 | 943 | 1.3E-5 |
| 6 | g11507.t1 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 948 | 982 | 3.7E-16 |
| 7 | g11507.t1 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 988 | 1018 | 6.1E-8 |
| 1 | g11507.t1 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 1021 | 1054 | 1.4E-8 |
| 8 | g11507.t1 | Pfam | PF00806 | Pumilio-family RNA binding repeat | 1064 | 1093 | 2.3E-6 |
| 39 | g11507.t1 | ProSiteProfiles | PS50303 | Pumilio homology domain (PUM-HD) profile. | 780 | 1117 | 136.717 |
| 37 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 800 | 835 | 11.044 |
| 35 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 836 | 871 | 10.81 |
| 30 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 872 | 907 | 11.3 |
| 34 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 908 | 943 | 10.204 |
| 36 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 944 | 979 | 10.88 |
| 32 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 980 | 1015 | 11.207 |
| 31 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 1016 | 1051 | 9.574 |
| 33 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 1055 | 1091 | 9.154 |
| 38 | g11507.t1 | ProSiteProfiles | PS50302 | Pumilio RNA-binding repeat profile. | 1092 | 1127 | 4.558 |
| 23 | g11507.t1 | SMART | SM00025 | pum_5 | 800 | 835 | 1.4E-6 |
| 20 | g11507.t1 | SMART | SM00025 | pum_5 | 836 | 871 | 1.9E-6 |
| 16 | g11507.t1 | SMART | SM00025 | pum_5 | 872 | 907 | 4.7E-7 |
| 19 | g11507.t1 | SMART | SM00025 | pum_5 | 908 | 943 | 1.7E-8 |
| 22 | g11507.t1 | SMART | SM00025 | pum_5 | 944 | 979 | 6.4E-9 |
| 18 | g11507.t1 | SMART | SM00025 | pum_5 | 980 | 1015 | 5.3E-8 |
| 17 | g11507.t1 | SMART | SM00025 | pum_5 | 1016 | 1051 | 5.7E-7 |
| 21 | g11507.t1 | SMART | SM00025 | pum_5 | 1056 | 1091 | 1.7E-6 |
| 13 | g11507.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 781 | 1114 | 9.78E-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.
