Sequence
atgc intronic sequence ATGC exonic sequencegtaagttctcatgttttatacttttgcttgttcatttctcttgtaattttgtaataatcttgtcttctttttccttaccctatacttctctctcagCCTGCTCAAATTGCTGGATGTAAAACAGTTGTTCTTGCAACTCCACCAAGTAAGGATGGAAGCATTTGTAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63890.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63890.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 5
------------------------------gtaagttctcatgttttatacttttgcttgttcatttctcttgtaattttgtaataatcttgtcttctttttccttacccta--tacttc-tctctcagCCTGCTCAAATTGCTGGATGTAAAACAGTTGTTCTTGCAACTCCACCAAGTAAGGATGGAAGCATTTGTAAG
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gtaagttgaatagatatttctgttcctcttatgcctttcaatgttctacaattttgatattgtaatt----tgtatatttgtatttatcttgtcagaattagctgacggttaattattttgtttaccagCCTGCACAAATTGCAGGATGTAAAACTATTGTTCTTGCAAATCCTCCAACTCGGGATGGCACTACATGCAAG
upper sequence: AT5G63890.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 5
------------------------------gtaagttctcatgttttatacttttgcttgttcatttctcttgtaattttgtaataatcttgtcttctttttccttaccctatacttctctctcagCCTGCTCAAATTGCTGGATGTAAAACAGTTGTTCTTGCAACTCCACCAAGTAAGGATGGAAGCATTTGTAAG
| | || ||||| |||| ||||| || | || | | | || | | | | || || | || ||| | || | |||||||| |||||||| ||||||||||| |||||||||||| ||| |||| | |||||| | | || |||
gtaagttgaatagacatttcagttcctcttatgactttcaatgttctataattttggttctgtatattggtatttatctagccaga--tttagctgatggttaattattttgta------taccagCCTGCACAAATTGCAGGATGTAAAACTATTGTTCTTGCAAATCCTCCAACTCGGGATGGCACTACATGCAAG
upper sequence: AT5G63890.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA08G08630.1 (Glycine max), 3'ss of exon 4
----------------gtaagttctcatgttttatacttttgcttgtt-catttctcttgtaattttgtaataatc-ttgtcttctt---tttccttaccctatacttctctc-----tcagCCTGCTCAAATTGCTGGATGTAAAACAGTTGTTCTTGCAACTCCACCAAGTAAGGATGGAAGCATTTGTAAG
| | ||| ||| || | | | | | || |||| ||| | | |||||| | |||| || ||| || || | || | | |||||||| || ||||||||||||||||| |||| ||||||||||| ||| | ||||||| | || || |||
gtaagttgaattgatgtctaactagtttgtagtattgttctccatcctatagttgcattgtgattgt-tgataatcatcatctttttggattttgttgatctttgattgttttatatgccagCCTGCACAGATTGCTGGATGTAAAACTATTGTCCTTGCAACTCCTCCAGCTCAGGATGGTACTATATGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaattttgtaataatcttgtcttctttttccttaccctatacttctctctcagCCTGCTCAAATTGCTGGATGTAAAACAGTTGTTCTTGCAACTCCACCAAGTAAGGATGGAAGCATTTGTAAG
tccttac putative branch site (score: 2)
tcttgtcttctttttc CT-rich tract
ttttgtaataatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttctcatgttttatacttttgcttgttcatttctcttgtaattttgtaataatcttgtcttctttttccttaccctatacttctctctcagCCTGCTCAAATTGCTGGATGTAAAACAGTTGTTCTTGCAACTCCACCAAGTAAGGATGGAAGCATTTGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG