Sequence
atgc intronic sequence ATGC exonic sequencegtaagagtcgagatcctctgactttagtttaagtggcaagagctgatagatctagtcacgtatttagctatgatgggttcaatcagcttgtgtcttgttctatatctgagttctgtttctgtaactatgtattttttggtaaaaggatttttacttttgttctctgtatattgaagTGCACGCAATGGAAGAGATGAAACTCACTGGAAATCATCTCAAAGGGTCACGTCCACTTTTGACATTCTCATCCAATTTTGATAAAGATGCGCACTGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52930.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G12700.2 (Glycine max), 3'ss of exon 5
gtaagagtcgagatcctctgactttagtttaagtggcaagagctgatagatctagtcac-gtatttagcta---tgatgggttcaatcagct-tgtgtcttgttctatat-ctgagttctg----tttctgtaactatgtattttttggtaaaaggattttt---acttttgttctctgtatattga-----agTGCACGCAATGGAAGAGATGAAACTCACTGGAAATCATCTCAAAGGGTCACGTCCACTTTTGACATTCTCATCCAATTTTGATAAAGATGCGCACTGGAA
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gtaatattt----tcatctgattattatcataaggtcaatacaatactattttgcttgctatgatgatgtagagtcttgatctctgtatactacattcatgattctgtctgctgaattatgattttttatgtttctctcaacttttttctggtatcattttgctgatctctgtttttcctccactgctttccagTGCACACAATGGAGGAATTGAAGCTAACTGGAAATCAACTAAAAGGTTCTCGTCCTATTTTGACATTTTCAGCAAATTTTGAAAAAGATGCACATTGGAA
upper sequence: AT1G52930.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 3
gtaagagtcgag---atcctctgactttagtttaagtggcaaga--gctgatagatctagtcacgtatttagctatgatgggttca--atcagcttgtgt--cttg----ttctatatctgagttct---gtttctgtaactatgtattttttggtaaaaggattt-ttacttt--tgttctctgtatattgaagTGCACGCAATGGAAGAGATGAAACTCACTGGAAATCATCTCAAAGGGTCACGTCCACTTTTGACATTCTCATCCAATTTTGATAAAGATGCGCACTGGAA
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gtaattttctgctctagtttcaagtattcatttgcatggtaatatgagttttagattgcctaatggacatatattttatgtattctgcatcattttttgtaccttggaactaacttatttaagtaagagggatcctttttcttaagattttaaggaagaacagctaattaatgagacatattttgtttattttagTGCACACTATGGAAGAGTTGAAGCTTACTGGGAATCATCTAAAAGGATCACGTCCTCTTTTGACTTTCTCAACCAATTTTGATAAGGACCCCCACTGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactatgtattttttggtaaaaggatttttacttttgttctctgtatattgaagTGCACGCAATGGAAGAGATGAAACTCACTGGAAATCATCTCAAAGGGTCACGTCCACTTTTGACATTCTCATCCAATTTTGATAAAGATGCGCACTGGAA
ctgtaac putative branch site (score: 3)
cttttgttctctgt putative PPT
tattttttggtaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagagtcgagatcctctgactttagtttaagtggcaagagctgatagatctagtcacgtatttagctatgatgggttcaatcagcttgtgtcttgttctatatctgagttctgtttctgtaactatgtattttttggtaaaaggatttttacttttgttctctgtatattgaagTGCACGCAATGGAAGAGATGAAACTCACTGGAAATCATCTCAAAGGGTCACGTCCACTTTTGACATTCTCATCCAATTTTGATAAAGATGCGCACTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG