Sequence
atgc intronic sequence ATGC exonic sequencegttaacaaaaacccttttggattcgttgtctattaagatattgtactttatatgtcagttgacctggttttcctctttccgccattttgtagGATCTTCGTCTTGTGAGAGACAAATTCACTCATGTTTCACGAGGATTTGCATTCGTGCATTTCTATTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54230.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54230.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G35510.1 (Glycine max), 3'ss of exon 9
---------------------gttaacaaa--aacccttttggattcgttgtctattaaga---------tattgtactttatatgtcagttgacctggttttcctctttccgccattttgtagGATCTTCGTCTTGTGAGAGACAAATTCACTCATGTTTCACGAGGATTTGCATTCGTGCATTTCTATTCG
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gttaggttactaaattgttgagctagttaactaatccttttactatgcctatgcattggaggggcagggttgttcttgtttatgttgccatttatatgctaagtagtgttattatctattacagGATCTGCGTCTTGTGAGAGACAAGTTTACTCATGTCTCAAGGGGATTTGCATTTGTACACTTTTATTCG
upper sequence: AT3G54230.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G18030.1 (Glycine max), 3'ss of exon 9
-----------------gttaacaaa--aacccttttggattcgttgtctattaa---------gatattgtactttatatgtcagttgacctggttttcctctttccgccattttgtagGATCTTCGTCTTGTGAGAGACAAATTCACTCATGTTTCACGAGGATTTGCATTCGTGCATTTCTATTCG
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gtttgattactagttgagctagttaattaatccttttactatgtttatgcattggtggggcagggttgttcttgtttatgttgcaatttatatgctaagtagtgttgttatctattacagGATCTGCGTCTTGTGAGAGACAAGTTTACTCATGTCTCAAGGGGATTTGCATTTGTACACTTTTATTCG
upper sequence: AT3G54230.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 3'ss of exon 9
gttaacaaaaacccttttggattcgttgtctattaagatattgtactttatatgtcagttgacctggttttcctctttccgccattttgtagGATCTTCGTCTTGTGAGAGACAAATTCACTCATGTTTCACGAGGATTTGCATTCGTGCATTTCTATTCG
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------gtactcaagtgtggttattttgttaatactggttttcaattttacatctt--ctaa---gtttttcttgctaattttaatttgcagGATCTTCGACTTGTTCGAGATAAATTCACTCATGTATCAAGGGGATTTGCATTTGTACATTTTCATTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgtactttatatgtcagttgacctggttttcctctttccgccattttgtagGATCTTCGTCTTGTGAGAGACAAATTCACTCATGTTTCACGAGGATTTGCATTCGTGCATTTCTATTCG
agttgac putative branch site (score: 4)
ttttcctctttccgcc putative PPT
tactttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaacaaaaacccttttggattcgttgtctattaagatattgtactttatatgtcagttgacctggttttcctctttccgccattttgtagGATCTTCGTCTTGTGAGAGACAAATTCACTCATGTTTCACGAGGATTTGCATTCGTGCATTTCTATTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT