Sequence
atgc intronic sequence ATGC exonic sequencegtaaatagatatcattactttgtttgatttttctctttttatggctaccttcatttgttattatactgcatatcattttacttgccaacagattcatttgtaacaaatgatcttatactattatcagGAATTGTGGTTCGTAATACACTTGTTGTGTATGATCGTGAGAATTCGAAGGTTGGATTCTGGAGAACCAATTGTTCGGAGTTATCGGATAGGCTTCATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G50050.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G05490.1 (Glycine max), 3'ss of exon 7
gtaaatagatatcatt-actttgtttgatttt-tctctttttatggctaccttcatttgttattatactgca-tatcattttacttgccaacagattcatttgtaaca----aatgatc-ttatactattatc-----agGAATTGTGGTTCGTAATACACTTGTTGTGTATGATCGTGAGAATTCGAAGGTTGGATTCTGGAGAACCAATTGTTCGGAGTTATCGGATAGGCTTCATAT
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----gtatatcttatttagtatgggtaatttcatgccatttcatactttcactcttttgaaatattgttcctctatgatttttgttagagttatgggtttgtgcaatactttagtgatcatcattcttttgtttgtgtagGCATTGTTGTTCGTAACACTCTTGTAATGTATGATCGTGAGCATTCAAAAATTGGTTTCTGGAAAACTAATTGTTCTGAGTTATGGGAAAGACTACATGT
upper sequence: AT3G50050.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G39800.1 (Glycine max), 3'ss of exon 10
gtaaatagatatcattactttgtttgatttttctctttttatggctaccttcatttgt--tattatactgcatatcattttacttgccaacagattcatttgtaaca-------aatgatcttatactattatcagGAATTGTGGTTCGTAATACACTTGTTGTGTATGATCGTGAGAATTCGAAGGTTGGATTCTGGAGAACCAATTGTTCGGAGTTATCGGATAGGCTTCATAT
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--gtatagcttatttagtataggttatttcatgccatttcgtacttccccttatttgaagtattgttcctc-tatgatttttgttagagttatgggtttgtgcaatactttagtgataattcttttgtttgtgtagGTATTGTTGTTCGTAACACTCTTGTAATGTATGATCGTGAGCATACAAAAATTGGTTTCTGGAAAACTAATTGTTCTGAGTTATGGGAAAGACTACATGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattttacttgccaacagattcatttgtaacaaatgatcttatactattatcagGAATTGTGGTTCGTAATACACTTGTTGTGTATGATCGTGAGAATTCGAAGGTTGGATTCTGGAGAACCAATTGTTCGGAGTTATCGGATAGGCTTCATAT
ttgtaac putative branch site (score: 2)
atcttatactattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatagatatcattactttgtttgatttttctctttttatggctaccttcatttgttattatactgcatatcattttacttgccaacagattcatttgtaacaaatgatcttatactattatcagGAATTGTGGTTCGTAATACACTTGTTGTGTATGATCGTGAGAATTCGAAGGTTGGATTCTGGAGAACCAATTGTTCGGAGTTATCGGATAGGCTTCATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA