Sequence
atgc intronic sequence ATGC exonic sequencegtatctctatttatgttcgtgttgttctattttttaacaaagatcaacattatacgggttgttttggaagGTTCGGGTTCCTACTGGGAAGATTGTTCTGGAATTACCTGCTGGAATGTTGGATGATGATAAAGGTGACTTTGTTGGTACTGCAGTTCGCGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G11980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G04150.1 (Glycine max), 3'ss of exon 4
--------------------------gtatctctatttatgttcgtgttgttctattttttaacaaagatcaacattatacgggttgtt-----ttggaagGTTCGGGTTCCTACTGGGAAGATTGTTCTGGAATTACCTGCTGGAATGTTGGATGATGATAAAGGTGACTTTGTTGGTACTGCAGTTCGCGAG
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gtagatgctggtgccttgctgtttttttttatttaattatattt-tataactggattttcatgttatggctattgttatgttggatattcttatttgtaagGCAAGGGTTCCTGTTGGAAGAATTATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTTCGTGAG
upper sequence: AT4G11980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G04160.1 (Glycine max), 3'ss of exon 4
-----------------gtatctctatttat-----gttcgtgttgtt--ct--attttttaacaaagatcaacattatacgggttgtt-----ttggaagGTTCGGGTTCCTACTGGGAAGATTGTTCTGGAATTACCTGCTGGAATGTTGGATGATGATAAAGGTGACTTTGTTGGTACTGCAGTTCGCGAG
|| | | | ||| | | | || || || ||||| | | | |||| |||| || || |||| |||||||| ||| | | || ||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||| || |||
gtagacactggtgccttgtgttttttttttttgagaaattatatttttaactggattttcattttatggctattcttatgttggttattcttatttataagGCAAGGGTTCCTGTTGGAAGAAACATTTTGGAATTGCCTGCTGGAATGTTGGATGATGACAAAGGTGATTTTGTTGGTACTGCAGTGCGTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcgtgttgttctattttttaacaaagatcaacattatacgggttgttttggaagGTTCGGGTTCCTACTGGGAAGATTGTTCTGGAATTACCTGCTGGAATGTTGGATGATGATAAAGGTGACTTTGTTGGTACTGCAGTTCGCGAG
ttttaac putative branch site (score: 2)
ttgtttt putative PPT
tattttttaacaaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctctatttatgttcgtgttgttctattttttaacaaagatcaacattatacgggttgttttggaagGTTCGGGTTCCTACTGGGAAGATTGTTCTGGAATTACCTGCTGGAATGTTGGATGATGATAAAGGTGACTTTGTTGGTACTGCAGTTCGCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG