Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcttattgtgcatgagatttgaagtagtggttgttttgatttagttagtatgctcattttcatggggatatctatttcttatgctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24090.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
--gtaatgcttattgtgcatgagatttgaagtagtggttgttttgatttagtt-agtatg-ctcattttcatggggatatctatttcttatgctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA------
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gcagaatagtcattat---cgcattacaaaataat--tcattctgactgaacccattatgacttctatttatggcagtccct-tacattatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT
upper sequence: AT3G24090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G47860.1 (Glycine max), 3'ss of exon 3
------gtaatgcttattgtgcatgagatttgaagtagtggttgttttgatttagttagtatgctcattttcatggggatatctatttcttat-gctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA
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ttatatgtaagctgcattttctgcttctcttagatgggtgtgaataacattatggtt--ttgggtgatgttagcttgaa-gtacatttccaattatcttgcagGAGGTCAGGTTGTTACCTTCAGTCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCCACATTATCCTAATGA
upper sequence: AT3G24090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 3
gtaatgcttattgtgcatg---agatttgaagtagtggttgttt-tgatttagttagtatgctcattttcatggggatatctatttcttat-gctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA
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-ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA
upper sequence: AT3G24090.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0064g00050.t01 (Vitis vinifera), 3'ss of exon 3
-------gtaatgcttattgtgcatgagatttgaagtagtggttgttttgatttagttagtatgctcattttcatggggatatctatttcttatgctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA
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tacagtagtgatgtttctc-tttaaagcgtcttttccatttcatataaaatctcaattacaatttagaatatgaggagagttgttaccttttatg--ttgcagGTGACCAGACTGTCACATTTAGTCAAGTTGTCCTTGAAGTTATGCGGCATCTTGAAGGAGCCTATGCTCTCATTTTCAAAAGTCGGCATTATCCAAATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatttagttagtatgctcattttcatggggatatctatttcttatgctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA
ttttgat putative branch site (score: 4)
tttcttat putative PPT
atatctatttcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcttattgtgcatgagatttgaagtagtggttgttttgatttagttagtatgctcattttcatggggatatctatttcttatgctttgtagGTGGACAAACTGTTACATTCTGTGAAGTTGTGTTTGAAGTGATGAGGCATCTTGAAGGAGCTTATGCTCTTATATTTAAAAGCTGGCATTATCCGAATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG