Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatcttaattcttcaggcttttacaagattcatcttctggaagagtgatctaaaccaagataatatgtccattatcctaaacaatattgcttttccgcagATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGACTTTGTAAGATCACTCAATGTTTTCCACCCCAATGCTTCTCTAGAAGACA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G17615.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G15900.1 (Glycine max), 3'ss of exon 2
gtaaaatcttaattcttcaggcttttacaagattcatcttctggaagagtgatctaa-accaagataatatgtccattatcctaaacaatattgc-ttttccgcagATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGACTTTGTAAGATCACTCAATGTTTTCCACCCCAATGCTTCTCTAGAAGACA
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------tattgctacttataaatatcttaaatgtcattttatgtcattcttgtgtggcatctctatgaagtaatctttcaattgactattgatatgctacttgcagATCTTTGATTTATTTGATGTCAAGAAGCTTGGAGTCGTTGACTTCGAAGACTTTGTCAGATCTCTCAATGTTTTCCACCCAAATGCTTCATTAAAAGACA
upper sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G05580.1 (Glycine max), 3'ss of exon 4
---gtaaa-atcttaattcttcaggcttttacaagattcatcttctggaagagtgatctaaaccaagataatatgtccattatcctaaacaatattgcttt----tccgcagATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGACTTTGTAAGATCACTCAATGTTTTCCACCCCAATGCTTCTCTAGAAGACA
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cttataaacatcttaaat----gacattttatg---tcagtcttgtgtggtatc--tcta---tgaaataatctttcaattgactaaatatccattgatatgctatgtgcagATCTTTGATTTATTTGATGTCAAGAAGAAGGGAGTCATTGACTTCGAAGACTTTGTTAGATCTCTGAATGTTTTCCACCCAAATGCATCATTAGAAGACA
upper sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0236g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaatcttaattcttcaggcttttacaagattcatcttctggaagagtgatctaaaccaagataatatgtccattatcc-taaacaatattgcttttccgcagATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGACTTTGTAAGATCACTCAATGTTTTCCACCCCAATGCTTCTCTAGAAGACA
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--atgcactgcaagcattattctttt-caccatttaaatacttctatttgttttgaaagtggaacaattttttaatcagaaattgggatcattgaactt--gcagATCTTTGATCTTTTTGATGTTAAGCGGAAGGGAGTCATTGATTTTGGTGACTTTGTCAGGTCACTAAATGTTTTCCATCCAAATGCCCCACAAGAAGACA
upper sequence: AT4G17615.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv02s0236g00150.t01 (Vitis vinifera), 3'ss of exon 4
gtaaaatcttaattcttcaggcttttacaagattcatcttctggaagagtgatctaaaccaagataatatgtccattatcctaaacaatattgcttttcc-gcagATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGACTTTGTAAGATCACTCAATGTTTTCCACCCCAATGCTTCTCTAGAAGACA
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--atgcactgcaagcattattctttt-caccatttaaatacttctatttgttttgaaattggaataattttttaatcaga--aattgggatcattaaacttgcagATCTTTGATCTTTTTGATGTTAAGCGGAAGGGAGTCATTGATTTTGGTGACTTTGTCAGGTCACTAAATGTTTTCCATCCAAATGCCCCACAAGAAGACAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86058729|gb|DR354486.1|DR354486EST: AACTTGCTTTGTTCAAAAGCCGGAAGAGGGAGAATATATTTGCTAATAGG ATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGAC
genomic: AACTTGCTTTGTTCAAAAGCCGGAAGAGGGAGAATATATTTGCTAATAGGgtaaaatctt ... ttttccgcagATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatctaaaccaagataatatgtccattatcctaaacaatattgcttttccgcagATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGACTTTGTAAGATCACTCAATGTTTTCCACCCCAATGCTTCTCTAGAAGACA
tcctaaa putative branch site (score: 2)
ttgcttttcc putative PPT
taaacaatatt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatcttaattcttcaggcttttacaagattcatcttctggaagagtgatctaaaccaagataatatgtccattatcctaaacaatattgcttttccgcagATATTTGATATGTTTGATGTTAAACGAAAAGGAGTCATCGATTTCGGGGACTTTGTAAGATCACTCAATGTTTTCCACCCCAATGCTTCTCTAGAAGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA