General information for g3383.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as G/T mismatch-specific thymine DNA glycosylase.
Parent gene
- The parent gene g3383 is located on chr_3: 25003947..25004947 (- 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 | g3383 | g3383.t1 | TTS | g3383.t1 | 24998695 | 24998695 |
| chr_3 | g3383 | g3383.t1 | isoform | g3383.t1 | 24999208 | 25003947 |
| chr_3 | g3383 | g3383.t1 | exon | g3383.t1.exon1 | 24999208 | 24999734 |
| chr_3 | g3383 | g3383.t1 | cds | g3383.t1.CDS1 | 24999208 | 24999734 |
| chr_3 | g3383 | g3383.t1 | exon | g3383.t1.exon2 | 24999802 | 25001164 |
| chr_3 | g3383 | g3383.t1 | cds | g3383.t1.CDS2 | 24999802 | 25001164 |
| chr_3 | g3383 | g3383.t1 | exon | g3383.t1.exon3 | 25001254 | 25001616 |
| chr_3 | g3383 | g3383.t1 | cds | g3383.t1.CDS3 | 25001254 | 25001616 |
| chr_3 | g3383 | g3383.t1 | exon | g3383.t1.exon4 | 25001713 | 25001842 |
| chr_3 | g3383 | g3383.t1 | cds | g3383.t1.CDS4 | 25001713 | 25001842 |
| chr_3 | g3383 | g3383.t1 | exon | g3383.t1.exon5 | 25001907 | 25002809 |
| chr_3 | g3383 | g3383.t1 | cds | g3383.t1.CDS5 | 25001907 | 25002809 |
| chr_3 | g3383 | g3383.t1 | exon | g3383.t1.exon6 | 25003367 | 25003947 |
| chr_3 | g3383 | g3383.t1 | cds | g3383.t1.CDS6 | 25003367 | 25003947 |
| chr_3 | g3383 | g3383.t1 | TSS | g3383.t1 | 25004970 | 25004970 |
Sequences
>g3383.t1 Gene=g3383 Length=3867
ATGGAGTCTTCCACTCCACCAATATCTTCTTCCGATAATAATAATCATCCTATGAATACA
ATTGCTCAAGATCCGCTCGCATTACCAACTGAGATTTCATCGTCTAGCCTATACAATAAT
AATAATAACAGTGGTAATAGCAGCAGCGGTAATAATGAAACTCGAACACATGATAGTGGA
AATTTAACGTCGTCTTTATCGACGGGGACAACAACCCAAAGCAATAGTAGCAATAATATT
AGTAACATAAGTGATAAAGAAAAAGAAAATCTCATTGATGGCACTATAAATAATAATAAT
AATAATGGCGCTATATATTCAAATGATATAACAATAAAACATGAAGAATCAAATTCATTG
ACAAATGACGATCGACGAATGCAATATGATTCCAACCAAATAGCAAATAATTATTCTAAT
AGTGACCCAAGAAAACTTAATCATCATCATCAACATCATATGAACATGCATGTACCACCA
CAACAACAGCATGAGCCGTCACACCATAAAACATTAAGTCATTCCATAGAAAATCTAAGT
AAAACGACAGAGAAATGTACATCTAATGAAAATATGAAAATGTATCCGAATCTAATAGAT
GGTCATGAATACGATGATGGCTATGAAACAGGTGTGAGTGACTTAATGTCACATAAATAT
AAACTTCCATCGCTACCACCGCCTTCATCCTCACCCTATTCATCTCTTTCATCGTCATCG
ATGTCAACCATTTCGACTGCGACGATGACACCAACAAATTTGGTAAATCCCCAACAACAA
CAATCGCCGTCATACATGAGTGGTAGTACAGGCAACGGAAATGCCGGAAATAATAATATG
AATCATTATCAATCGATGCAACAACAACAGCAGCAATATCAAGTCATACAGCAGCAGCAG
CAACAATATCAAGCAATGCAACATTCTAACCATATGAATTCTTTTAATTATCATCATCCA
ATGTTTAGAATGCAGCAGCAACAACAACAATCAGCTCATCAACTCGCGAATGTTGTAAAA
ACTGAACCGCCAGCTAATAATGATCCATCATTAATTACTGATGATCCTTATCGTTTTGTG
GATGAAGATTTGTCAAATGGAATGAGTACAGGTCAGGCACTTCATAATTCAATACATCAA
AATCAGCAACAGCAGCACATGTCATCTCCTGTAATGTCAAATAGCAATTATTCAGCATCC
TCTTCTCCAATGCCATCACAACAACAACAGTCACAAAGTGGAGGCGGAAATGCATCGTTG
TTGCAATTCAATGAACATCACATGTCACCCCATCATATGAACCCTGTTAATTATATGAAC
CATCAGCAACATATACAATCACAACACAATTTAATGAATGGAAATGTTCATGAAAATTCT
GGTCACAGTCATGGGGGAATAAACACAAATAACATGAATATGATGATGATGAATGATACA
CCAAAAAAGCGAGGTCGCAAAAAGAAGTTACGAGATGAAAATGGTAATCCAATTGAAGAT
AGTAGACCAACAAAAGAACGAAAAAAGCATGATCGATTTAATGGTATGCCAGAGGAAGAA
GTCACAAAACGTGTTATACCAGATCATCTTACTAATAATCTTGATGTTGTTATCGTCGGA
ATTAATCCAGGTCTTTTTGCTGCATATAAGGGCCATCATTATGCGGGTCCTGGAAATCAT
TTCTGGAAGTGTCTCTATCTATCTGGACTAACTTCTGTGCAAATGACAGCTGAGGAGGAT
TATAAATTACTACATTGTGGCATTGGTTTTACGAATATGGTGCAAAGACCTACAAAAGGT
AGTGCAGATTTAACTCGTAAAGAAATTAAAGAAGGTTCTCGAATTTTACTCGAAAAATTG
CAAAAATATCAACCAAAAATTGCTGTCTTTAATGGAAAACTCATCTTTGAAGTGTTTAGT
GGCAAAAAAGACTTTTGTTTTGGCAAACAACCCGAGACAGTTGAAGGAACAAATACATAT
ATGTGGGTAATGCCATCATCAAGTGCAAGATGTGCCCAATTGCCAAGAGCAGCTGATAAG
GTCCCATTTTATGCGGCGCTTAAAAAATTTAGAGATTATTTAAATGGTCTTGTACCAGAA
TATGATGAAAGCGAATATGTATTTAATGATCCAAAATATAATCAAATTAGTACTGAAGCG
GAACTAAAAGATGATGCACTTGCTTCATTTACAACACTAGAAAATGGTGAAATTGTAGCA
ATAGACTCAAATAAAAAGAAACGTGGACGACCTAAGAAAGTGCGCGGTGAAAATGGCGAA
GAAATTGTAGCAACGCCAAGACGAAAACAAAATACTGAACTCAATCAGGATGGCTTAGAA
GATGATCCAAGTAAAAAGAAACGTGGCCGCCCAAAGAAAAATAAAGATGGAACAACAACT
TCTTCAACAAATAACCGAAAAAAGAGCAATAAAGAAAAGCAACAACCTTCACCATTAAAT
AGTGGCAATGAATTGAGTTCGATGTCCCTTCATCATCATCATTCATCATCGCCTATCTTA
CAAAATCCCCAAATGTCTAGTCTATCGAATAATATTGGAAGCAATAGTAATACAGGATCA
TCGTCAACACCTTCGTCTTCATTCTTGCCACCTATTGATTCTCCATCGGGCATTAGTTAT
CAAAATGGTGCTATAAATCAACAGCAAACGAACCTTCAAACACAATCTCCTGCAGGTCAC
TGTTTTTCTTCATCGAATTCAATCAATGAGCATGTGTCACAGCCAGAAATTTCACCACAT
CAGACATATCAGAGACAGGCAAATGCTCAACAAATGTATAATACAACTACACCCGAAATA
ACTTCTGATCAAATAAATTCGCCTGTAAATGCTGTGCCCTCACCTAGTCTAGCACCATCA
GATTTTGAACCGCCACAAAATACAAATGACCTTGATCCATACTCACAGCAGCAGTCTGAA
CCGCATTCGCAATCGCCATTGTCTCAATCGCTTTATCCACATCATCAACAGCAAGCAATG
TCGCAAATGATGAATAATGTCAGCAATAGTCCCGTATATTCACCATATTCAAGGCAACAG
TCACAGCAGCAACAGCAACAAACTCCTCAGCAAAACTACATGCAATCACCACATCATACG
CAACAGCAATCTCCAGTAGTGACTCCTCAAAATAACTCTGTAAATAGTAACAAATCAATT
GGACAACCGCAACATATTAATGGCACATCACAAACTAGCGGTGATATGTTTAAAGATGTC
GCTACAAAAAGTCTTTCGGGCCTCGAGTCCTTAGTCGATCAAATACCAAATATTAATGAA
CAAGACACAGGTCTAAGTGCGCTTTCTGGAGCACAAAATGTTCAACATCAACTTAACGAC
TATTCTAACATGCTTTCTGGTTATTCCTCCTCATCAGGCACTACAGCATCATCAAATTTG
ACTCCAGTTTCGACAGCACTTGGCTCTTCATCGCTTCTACCGCCATCAATAGGCGCTCCT
CATCCACATTATCCTTATACATCACATGCTACTGCAACTCAATCGCCCTATTCAGCAAAT
CCATTCTCTGTAAGTAGTTTGACATCATCGAATTATCCTTCGGCAGCTGCAGCAGCAATG
AATAGTTATCATCAAAATCTAATGGGAACGAGTCATTTAACGTCATCTTTTATGGAACCA
CATATGCCAGTTCCTGTTACGCCTCTTTATCATTCTTATCAACAACAAGGCTATCCTGGT
TATCCTGCACCTCCTCATCATCATCCTTCAGCTGCAGCAGCCGCTTTACATATGTCAAAC
TATCCCTATTACACAAACACAGGCTACACACAAGCACCTGGCAGCCATTCAACGTACCAT
TCAATGTTTGACAGAATAAACTTTTGA
>g3383.t1 Gene=g3383 Length=1288
MESSTPPISSSDNNNHPMNTIAQDPLALPTEISSSSLYNNNNNSGNSSSGNNETRTHDSG
NLTSSLSTGTTTQSNSSNNISNISDKEKENLIDGTINNNNNNGAIYSNDITIKHEESNSL
TNDDRRMQYDSNQIANNYSNSDPRKLNHHHQHHMNMHVPPQQQHEPSHHKTLSHSIENLS
KTTEKCTSNENMKMYPNLIDGHEYDDGYETGVSDLMSHKYKLPSLPPPSSSPYSSLSSSS
MSTISTATMTPTNLVNPQQQQSPSYMSGSTGNGNAGNNNMNHYQSMQQQQQQYQVIQQQQ
QQYQAMQHSNHMNSFNYHHPMFRMQQQQQQSAHQLANVVKTEPPANNDPSLITDDPYRFV
DEDLSNGMSTGQALHNSIHQNQQQQHMSSPVMSNSNYSASSSPMPSQQQQSQSGGGNASL
LQFNEHHMSPHHMNPVNYMNHQQHIQSQHNLMNGNVHENSGHSHGGINTNNMNMMMMNDT
PKKRGRKKKLRDENGNPIEDSRPTKERKKHDRFNGMPEEEVTKRVIPDHLTNNLDVVIVG
INPGLFAAYKGHHYAGPGNHFWKCLYLSGLTSVQMTAEEDYKLLHCGIGFTNMVQRPTKG
SADLTRKEIKEGSRILLEKLQKYQPKIAVFNGKLIFEVFSGKKDFCFGKQPETVEGTNTY
MWVMPSSSARCAQLPRAADKVPFYAALKKFRDYLNGLVPEYDESEYVFNDPKYNQISTEA
ELKDDALASFTTLENGEIVAIDSNKKKRGRPKKVRGENGEEIVATPRRKQNTELNQDGLE
DDPSKKKRGRPKKNKDGTTTSSTNNRKKSNKEKQQPSPLNSGNELSSMSLHHHHSSSPIL
QNPQMSSLSNNIGSNSNTGSSSTPSSSFLPPIDSPSGISYQNGAINQQQTNLQTQSPAGH
CFSSSNSINEHVSQPEISPHQTYQRQANAQQMYNTTTPEITSDQINSPVNAVPSPSLAPS
DFEPPQNTNDLDPYSQQQSEPHSQSPLSQSLYPHHQQQAMSQMMNNVSNSPVYSPYSRQQ
SQQQQQQTPQQNYMQSPHHTQQQSPVVTPQNNSVNSNKSIGQPQHINGTSQTSGDMFKDV
ATKSLSGLESLVDQIPNINEQDTGLSALSGAQNVQHQLNDYSNMLSGYSSSSGTTASSNL
TPVSTALGSSSLLPPSIGAPHPHYPYTSHATATQSPYSANPFSVSSLTSSNYPSAAAAAM
NSYHQNLMGTSHLTSSFMEPHMPVPVTPLYHSYQQQGYPGYPAPPHHHPSAAAAALHMSN
YPYYTNTGYTQAPGSHSTYHSMFDRINF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3383.t1 | CDD | cd10028 | UDG-F2_TDG_MUG | 526 | 688 | 2.5237E-74 |
| 5 | g3383.t1 | Coils | Coil | Coil | 286 | 306 | - |
| 4 | g3383.t1 | Gene3D | G3DSA:3.40.470.10 | - | 508 | 703 | 5.8E-76 |
| 14 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 43 | 85 | - |
| 10 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 223 | 244 | - |
| 13 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 377 | 416 | - |
| 19 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 481 | 513 | - |
| 17 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 490 | 513 | - |
| 12 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 742 | 840 | - |
| 11 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 753 | 787 | - |
| 18 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 814 | 840 | - |
| 15 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 909 | 928 | - |
| 16 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 972 | 999 | - |
| 9 | g3383.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1011 | 1052 | - |
| 2 | g3383.t1 | PANTHER | PTHR12159 | G/T AND G/U MISMATCH-SPECIFIC DNA GLYCOSYLASE | 297 | 719 | 8.1E-112 |
| 1 | g3383.t1 | Pfam | PF03167 | Uracil DNA glycosylase superfamily | 529 | 680 | 4.1E-19 |
| 7 | g3383.t1 | SMART | SM00384 | AT_hook_2 | 745 | 757 | 1.7 |
| 8 | g3383.t1 | SMART | SM00384 | AT_hook_2 | 785 | 797 | 0.96 |
| 3 | g3383.t1 | SUPERFAMILY | SSF52141 | Uracil-DNA glycosylase-like | 526 | 691 | 1.48E-39 |
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:0006285 | base-excision repair, AP site formation | BP |
| GO:0003677 | DNA binding | MF |
| GO:0000700 | mismatch base pair DNA N-glycosylase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K20813 (thymine-DNA glycosylase)
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.
