Sequence
atgc intronic sequence ATGC exonic sequencegtatgttttctttactttgcttttaagccaattatctgtatcttgttttgattcttcatttttgtttccagtcgtgattttataacatcttctcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G22310.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G22310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
----gtatgttttctttactttgcttttaagccaattatctgtatcttgttttgattcttcatttttgtttccagtcgtgattttataacatcttctcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT
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ggactaaaagatagtaaaccctatttttatttagaaaaacta------gttaaggaaacttcttgctggatttttttttgtctcctaaagatatatcctttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
upper sequence: AT3G22310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G45030.1 (Glycine max), 3'ss of exon 4
--gtatgttttctttactttgcttttaagccaattatctgtatcttgttttgattcttcatttttgtttccagtcgtgattttataacatcttctcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT
| | | || | |||||| | | || || | || || | | | || | || || | || ||||||||| ||||||||||| || ||||| || || ||||||||||||||||| ||||| | | | || |||||| ||| ||||||||| ||||
ctaaaaagatagtagaccctatttttaattagaaaaactag---ttaaggaagctttttgttaaaggatttt-ttgtctctcctaaagatatgtcgtttgttagGAACATGCAAAAGGAGGAAAGTGTATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCGTATGCCATGGCAAGAAGTGTTAAATGTGAGGCTT
upper sequence: AT3G22310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------gtatgttttctttacttt---gctttt----aagccaatta---tctgtatcttgttttgattc---ttcatttttgtttccagtcgtgatttta----taacatcttc----tcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT
|| ||||||| || || | |||| | || | || || | | || |||| || | |||| |||| || | |||| || || | | | || ||||||||| ||||| |||||||| ||||| || || ||||||||||| ||||| ||||| | |||| || |||||| || || | |||||| |||
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttgcttttacctcca-tcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattcttcatttttgtttccagtcgtgattttataacatcttctcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT
ttataac putative branch site (score: 2)
catcttctcctttac CT-rich tract
attttataacatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttttctttactttgcttttaagccaattatctgtatcttgttttgattcttcatttttgtttccagtcgtgattttataacatcttctcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC