Sequence
atgc intronic sequence ATGC exonic sequencegcttgactttgttgagcattcttttgtccaaaaccgcataaaattcagaagattagatggtacaatgtctctagtagcaagagacatagctgtaaaagaattcaacaatgatccagacatattatatgttttgcattcaaagaatctcatttttacgtttctcaaagacaaatgtaatgattatgaaacagGTGCGATGTTGATGTCTCTTAAAGCTGGAAACCTTGGATTGAATATGGTAGCTGCAAGTCATGTCATTCTACTGGACCTATGGTGGAATCCAACAACAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16600.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G43430.1 (Glycine max), 3'ss of exon 10
gcttgactttgttgagcattcttttgtccaaaaccgcataaaattcagaagattagatggtacaatgtctctagtagcaagagacatagctgtaaaagaattcaacaatgatccagacatattatatgttttgcattcaaagaatctcattttt-----acgtttctcaaagacaaat-gtaatgattatgaaacagGTGCGATGTTGATGTCTCTTAAAGCTGGAAACCTTGGATTGAATATGGTAGCTGCAAGTCATGTCATTCTACTGGACCTATGGTGGAATCCAACAACAGA
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--------------------------------------------------------------------------------------------ttttccaactccttgaacttgcat-tatctactgtgttctacagttctagtgtctcaacctcggtagactttggtgtctgactagttgaaatttgtttcagATTGCTGTTATGCTGATGTCACTAAAAGCAGGAAACCTTGGTTTGAATATGGTTGCTGCATGTCATGTTATACTTTTGGATCTTTGGTGGAATCCAACAA----
upper sequence: AT3G16600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G23390.1 (Glycine max), 3'ss of exon 8
gcttgactttgttgagcattcttttgtccaaaaccgcataaaattcagaagattagatggtacaatgtctctagtagcaagagacatagctgtaaaagaattcaacaatgatccagacatattatatgttttgcattcaaagaatctcatttttacgtttctcaaagac-----aaatgtaatgattatgaaacagGTGCGATGTTGATGTCTCTTAAAGCTGGAAACCTTGGATTGAATATGGTAGCTGCAAGTCATGTCATTCTACTGGACCTATGGTGGAATCCAACAACAGA
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--------------------------------------------------------------------------------------------tcagtatgttttccaactccttgaacttgaattttctactgtgttctagtgtcttaaccttggtagactttggtgtctgactaattgaaatttgtttcagATAACTGTTATGCTGATGTCACTAAAAGCAGGAAACCTTGGTTTGAATATGGTTGCTGCATGTCATGTTATTCTTTTGGATCTTTGGTGGAATCCGACAA----
upper sequence: AT3G16600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S132_19V6.1 (Physcomitrella patens), 3'ss of exon 9
gcttgactttgttgagcattcttttgtccaaaaccgcataaaattcagaagattagatggtacaatgtctctagtagcaagagacatagctgtaaaagaattcaacaatgatccagacatattatatgttttgcattcaaagaatctca--tttttacgtttctcaaagacaaatgtaatgattatgaaacagGTG----CGATGTTGATGTCTCTTAAAGCTGGAAACCTTGGATTGAATATGGTAGCTGCAAGTCATGTCATTCTACTGGACCTATGGTGGAATCCAACAACAGA
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-----------------------------------------------------------gtatgcttttatctttccccatgggattagtggtat----ttttcctttctaccaaagctcatgctatgtct-acagttaataaatgcgagtcttttgcgaatcttacttgtgcttataatgaacttgttgcagGTGACAGTCATGATTATGTCTCTGAAAGCTGCAAGCCTTGGGCTTAATATGGTGGCTGCAAACCATGTGCTCCTACTGGACGTATGGTGGAATCCCACCA----
upper sequence: AT3G16600.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S3_639V6.1 (Physcomitrella patens), 3'ss of exon 9
gcttgactttgttgagcattcttttgtccaaaaccgcataaaattcagaagattagatggtacaatgtctctagtagcaagagacatagctgtaaaagaattcaacaatgatccagacatattatatgttttgcattcaaagaatctcatttttacgtttctcaaagacaaatgtaatgattatgaaacagGTG----CGATGTTGATGTCTCTTAAAGCTGGAAACCTTGGATTGAATATGGTAGCTGCAAGTCATGTCATTCTACTGGACCTATGGTGGAATCCAACAACAGA
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---------------------------------------------------------------gtttgctcttgtt-ctggtgaaactggtgttgcctt-tccatcaa--atct---cttcctatatcggtaggatgcaaatag-ctcgtctt-gtggtattctaatgtggttgtaatggaattgttacagGTGACGGTCATGATTATGTCTCTTAAAGCTGCAAGTCTAGGATTGAATATGGTGGCTGCAAGTCATGTGCTTTTATTGGACGTATGGTGGAATCCCACCA---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaagaatctcatttttacgtttctcaaagacaaatgtaatgattatgaaacagGTGCGATGTTGATGTCTCTTAAAGCTGGAAACCTTGGATTGAATATGGTAGCTGCAAGTCATGTCATTCTACTGGACCTATGGTGGAATCCAACAACAGA
aaatgtaatgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttgactttgttgagcattcttttgtccaaaaccgcataaaattcagaagattagatggtacaatgtctctagtagcaagagacatagctgtaaaagaattcaacaatgatccagacatattatatgttttgcattcaaagaatctcatttttacgtttctcaaagacaaatgtaatgattatgaaacagGTGCGATGTTGATGTCTCTTAAAGCTGGAAACCTTGGATTGAATATGGTAGCTGCAAGTCATGTCATTCTACTGGACCTATGGTGGAATCCAACAACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA