General information for g3549.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein groucho.
Parent gene
- The parent gene g3549 is located on chr_3: 26389859..26390336 (- 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 | g3549 | g3549.t1 | isoform | g3549.t1 | 26316219 | 26389894 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon1 | 26316219 | 26316326 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS1 | 26316219 | 26316326 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon2 | 26316386 | 26316585 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS2 | 26316386 | 26316585 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon3 | 26316642 | 26317065 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS3 | 26316642 | 26317065 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon4 | 26317127 | 26317376 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS4 | 26317127 | 26317376 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon5 | 26317450 | 26317703 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS5 | 26317450 | 26317703 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon6 | 26317768 | 26317953 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS6 | 26317768 | 26317953 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon7 | 26318501 | 26318557 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS7 | 26318501 | 26318557 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon8 | 26319879 | 26319983 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS8 | 26319879 | 26319983 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon9 | 26320038 | 26320241 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS9 | 26320038 | 26320241 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon10 | 26326793 | 26326825 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS10 | 26326793 | 26326825 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon11 | 26327126 | 26327263 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS11 | 26327126 | 26327263 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon12 | 26336341 | 26336385 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS12 | 26336341 | 26336385 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon13 | 26344880 | 26344943 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS13 | 26344880 | 26344943 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon14 | 26348308 | 26348402 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS14 | 26348308 | 26348402 |
| chr_3 | g3549 | g3549.t1 | exon | g3549.t1.exon15 | 26389859 | 26389894 |
| chr_3 | g3549 | g3549.t1 | cds | g3549.t1.CDS15 | 26389859 | 26389894 |
| chr_3 | g3549 | g3549.t1 | TSS | g3549.t1 | 26390402 | 26390402 |
| chr_3 | g3549 | g3549.t1 | TTS | g3549.t1 | NA | NA |
Sequences
>g3549.t1 Gene=g3549 Length=2199
ATGTATCCGACACCTCAGCGTCATCCCTCGTCTGCGGGACCGCCGCCACAGGGTCCAATC
AAATTTACAATAGCAGACACATTAGAAAGGATTAAAGAAGAATTTAATTTCCTACAAGCA
CAATATCACTCACTTAAATTAGAATGTGAAAAATTAGCAAGTGAAAAAACAGAAATGCAA
AGACATTATGTAATGTATTATGAGATGTCATATGGATTAAATGTGGAAATGCACAAACAG
ACGGAGATAGCAAAAAGACTAAATGCTTTAATTGGACAGCTTTTGCCGTTTTTAGCAGCC
GAACATCAACAACAAGTGGCACAAGCTGTAGAGCGTGCGAAGCAAGTGACGATGCCGGAA
CTAAATGCAATCATTGGGCAGCATCAACAACAGGGAATTCAACAACTCCTTCAACAAATT
CATGCACAACAGATTCCAGGTGCTCCTCCACAACCTATGCCATCATTAGGTGCACTTGGA
CCATTGGGAGCATTTGCAGCAGCTGGACCAATGGGTGGTTTGCCACATGGACCACAGAGT
TTATTGAAAAATCCACAAGATCTTCATCGCGAGGATATTAAGCCACTTGCAGGACCTTCA
GCAGAAGAAAGATTGAGGAATTCAGTATCGCCAGCTGATCGAGAAAAGTATCGTCCACGT
TCTCCACTTGATATCGATTCAGAAGCAAAACGTCGAAAAGAAGAAATTAAAGTGAATCAT
GAGAGCGATGGTGAAAAAAGTGATCAGGATTTAGTTGTGGACATCGCAAATGAAACGGGT
TCACCTTCACCTCGAGCAAATGGCGATCATTCAGAATCACGTGATCGTGACAGCATTGGA
CTCAATGGTGATCGAAATGGAGAAAAAGCTGGCACAAGTAAATTAAATAATGTTAATGAT
CGTCCACCCTCACGTTCTGGTTCAAGTTCATCACGCTCAACACCAAATCTCAAAACAAAA
GATCTCGATAAACCTGGAACTCCAGGAGCGAAAGCACGTTCAACAACACCAAATTCAACG
CCAGGCGTCCCACCGAAAGCTGTTATTCCATCATCACCTGCTGGCTATCCTTCATCTTCA
CCATATCAGCGACCAGCTGATCCATATCAACGACCACCGCCTGATCCTTATGGTCGTATA
CAACCACTCGGTTATGATCCACATTCACATGTTCGAACAAATGGAATACCTAATTTACCT
GGAGTTGGCGGCAAACCAGCATATTCATTTCATGTAAATGCTGAAAATCATTTAACACCT
GTGCCCTTTCCACCTGATGCATTAAGTGGTCCTGGAATCCCGCGACAAGCACGTCAAATC
AATACATTATCTCATGGTGAAGTTGTGTGTGCAGTGACGATATCAAATCCAACTAAATAT
GTTTATACTGGTGGTAAAGGATGTGTAAAAGTATGGGATATTTCACAACCAGGCAACAAA
AGTCCCGTCAGTCAACTTGATTGTTTGCAACGAGACAATTACATTCGTTCTGTGAAACTT
CTGCCTGATGGACGTACATTAATTGTTGGTGGTGAAGCATCAAATTTGAGTATTTGGGAT
TTAGCGAGTCCAACACCGCGAATTAAAGCCGAACTCACTTCAGCTGCACCAGCTTGTTAC
GCCTTAGCTATCTCACCCGATTCCAAAGTATGTTTCTCATGCTGTAGTGATGGAAATATT
GCAGTATGGGATCTTAACAATCAGACATTAGTGCGACAATTCCAAGGGCATACAGATGGA
GCATCATGCATTGACATTAGTCCTGATGGTTCAAAATTGTGGACTGGTGGATTGGATAAT
ACAGTAAGATCATGGGATTTAAGAGAAGGACGGCAACTGCAACAACATGATTTTAGTTCA
CAAATATTTTCATTAGGCTATTGTCCTACAGGTGATTGGTTAGCAGTTGGAATGGAAAAT
TCACATGTGGAAGTGCTGCATGCACAGAAAACAGAAAAATATCAATTGCATTTGCATGAA
AGTTGCGTCCTTTCTCTACGTTTTGCAACATGTGGCAAGTGGTTTGTATCAACGGGTAAA
GATAATTTATTGAATGCATGGCGAACACCTTATGGAGCCAGCATATTTCAGTCAAAAGAA
ACATCTTCGGTGCTCAGCTGTGACATTTCAACTGACGATAAGTACATTGTTACTGGATCA
GGAGACAAGAAAGCGACCGTATATGAGGTCATGTATTAA
>g3549.t1 Gene=g3549 Length=732
MYPTPQRHPSSAGPPPQGPIKFTIADTLERIKEEFNFLQAQYHSLKLECEKLASEKTEMQ
RHYVMYYEMSYGLNVEMHKQTEIAKRLNALIGQLLPFLAAEHQQQVAQAVERAKQVTMPE
LNAIIGQHQQQGIQQLLQQIHAQQIPGAPPQPMPSLGALGPLGAFAAAGPMGGLPHGPQS
LLKNPQDLHREDIKPLAGPSAEERLRNSVSPADREKYRPRSPLDIDSEAKRRKEEIKVNH
ESDGEKSDQDLVVDIANETGSPSPRANGDHSESRDRDSIGLNGDRNGEKAGTSKLNNVND
RPPSRSGSSSSRSTPNLKTKDLDKPGTPGAKARSTTPNSTPGVPPKAVIPSSPAGYPSSS
PYQRPADPYQRPPPDPYGRIQPLGYDPHSHVRTNGIPNLPGVGGKPAYSFHVNAENHLTP
VPFPPDALSGPGIPRQARQINTLSHGEVVCAVTISNPTKYVYTGGKGCVKVWDISQPGNK
SPVSQLDCLQRDNYIRSVKLLPDGRTLIVGGEASNLSIWDLASPTPRIKAELTSAAPACY
ALAISPDSKVCFSCCSDGNIAVWDLNNQTLVRQFQGHTDGASCIDISPDGSKLWTGGLDN
TVRSWDLREGRQLQQHDFSSQIFSLGYCPTGDWLAVGMENSHVEVLHAQKTEKYQLHLHE
SCVLSLRFATCGKWFVSTGKDNLLNAWRTPYGASIFQSKETSSVLSCDISTDDKYIVTGS
GDKKATVYEVMY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g3549.t1 | CDD | cd00200 | WD40 | 444 | 729 | 7.41623E-44 |
| 14 | g3549.t1 | Coils | Coil | Coil | 28 | 55 | - |
| 13 | g3549.t1 | Gene3D | G3DSA:2.130.10.10 | - | 400 | 732 | 2.2E-145 |
| 26 | g3549.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 195 | 370 | - |
| 28 | g3549.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 207 | 252 | - |
| 25 | g3549.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 268 | 283 | - |
| 27 | g3549.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 289 | 316 | - |
| 5 | g3549.t1 | PANTHER | PTHR10814:SF4 | TRANSDUCIN-LIKE ENHANCER PROTEIN 2 | 7 | 732 | 1.2E-296 |
| 6 | g3549.t1 | PANTHER | PTHR10814 | TRANSDUCIN-LIKE ENHANCER PROTEIN | 7 | 732 | 1.2E-296 |
| 11 | g3549.t1 | PRINTS | PR01850 | Groucho/transducin-like enhancer protein signature | 631 | 653 | 1.8E-54 |
| 8 | g3549.t1 | PRINTS | PR01850 | Groucho/transducin-like enhancer protein signature | 654 | 672 | 1.8E-54 |
| 10 | g3549.t1 | PRINTS | PR01850 | Groucho/transducin-like enhancer protein signature | 673 | 692 | 1.8E-54 |
| 9 | g3549.t1 | PRINTS | PR01850 | Groucho/transducin-like enhancer protein signature | 693 | 712 | 1.8E-54 |
| 7 | g3549.t1 | PRINTS | PR01850 | Groucho/transducin-like enhancer protein signature | 713 | 732 | 1.8E-54 |
| 1 | g3549.t1 | Pfam | PF03920 | Groucho/TLE N-terminal Q-rich domain | 7 | 134 | 5.7E-68 |
| 4 | g3549.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 442 | 473 | 0.097 |
| 3 | g3549.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 540 | 564 | 0.16 |
| 2 | g3549.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 570 | 606 | 0.0019 |
| 24 | g3549.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 551 | 565 | - |
| 23 | g3549.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 593 | 607 | - |
| 29 | g3549.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 442 | 615 | 26.92 |
| 32 | g3549.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 532 | 573 | 9.606 |
| 33 | g3549.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 574 | 615 | 15.588 |
| 30 | g3549.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 656 | 732 | 9.626 |
| 31 | g3549.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 656 | 687 | 8.503 |
| 22 | g3549.t1 | SMART | SM00320 | WD40_4 | 436 | 473 | 0.024 |
| 16 | g3549.t1 | SMART | SM00320 | WD40_4 | 482 | 520 | 0.14 |
| 19 | g3549.t1 | SMART | SM00320 | WD40_4 | 525 | 564 | 4.4E-4 |
| 18 | g3549.t1 | SMART | SM00320 | WD40_4 | 567 | 606 | 2.0E-9 |
| 17 | g3549.t1 | SMART | SM00320 | WD40_4 | 609 | 647 | 53.0 |
| 20 | g3549.t1 | SMART | SM00320 | WD40_4 | 649 | 688 | 0.0094 |
| 21 | g3549.t1 | SMART | SM00320 | WD40_4 | 689 | 729 | 0.28 |
| 12 | g3549.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 434 | 729 | 5.27E-65 |
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:0005634 | nucleus | CC |
| GO:0005515 | protein binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K04497 (groucho)
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.
