Sequence
atgc intronic sequence ATGC exonic sequencegtaattataacacttggtttcttttttttacatggtggtgagtgactggtacgtgagtctaataatccaatgatataagtgtgtgtatgaatatatgaaagGTTAAATGGAGGTAAATTGCTTGAGATGATTAGAGGAAGAAGGCTAGTGTTTGTTGGAGATTCGCTGAATAGAAACATGTGGGAGTCTTTGGTTTGCATT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12060.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G033805_T01 (Zea mays), 3'ss of exon 1
gtaattataacacttggtttcttttttttacatggtggtgagtgactggtacgtgagtctaataatccaatgatataagtgtgtgtatgaatatatgaaagGTTAAATGGAGGTAAATTGCTTGAGATGATTAGAGGAAGAAGGCTAGTGTTTGTTGGAGATTCGCTGAATAGAAACATGTGGGAGTCTTTGGTTTGCATT
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gtgaggataaggtt--actggaacaatgca-atggttttaattattt--catttcaatcttggtttgtaatttgtcaagttcatgtttgtgt-catttcagATTGAACCCAACCGATATGTTGGAGAGGCTGAGAGGAAAAAGACTGGTGTTCGTTGGTGATTCGCTCAATAGGAACATGTGGGAATCCCTTGTGTGTATT
upper sequence: AT3G12060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G30210.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------gtaattataacact-tggtttcttttttttacatggtggt--gagtgactggtacgtgagtctaataatccaatgatataagtgtgtgtatgaat--atatgaaagGTTAAATGGAGGTAAATTGCTTGAGATGATTAGAGGAAGAAGGCTAGTGTTTGTTGGAGATTCGCTGAATAGAAACATGTGGGAGTCTTTGGTTTGCATT
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gtaaagtttttaacttcatgggtgtttatgtttttgtccaaaattgacaatattttgtctattttattttggtaatgtgaatttgttgtcttgtattatacttgaattgattcatttgctaattttctt-ttggggggtcccaaaatttggttgaattggtaatatagGTTGGATGCGCATCGAATGCTGCAATTGTTGAGAGGGAAACGACTGGTTTTTGTTGGCGATTCGCTCAATAGGAACATGTGGGAGTCTTTGATTTGCATA
upper sequence: AT3G12060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G33110.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------------------------gtaattataacacttggtttcttttttttacatggtggtgagtgactggtacgtgagtctaataatccaatgatataagtgtgtgtatgaatatatgaaa--gGTTAAATGGAGGTAAATTGCTTGAGATGATTAGAGGAAGAAGGCTAGTGTTTGTTGGAGATTCGCTGAATAGAAACATGTGGGAGTCTTTGGTTTGCATT
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gtatgcaaatctgttttaatttgttggttagttttagatggtaaagcttttaatttgatgggtgtttgtccaaaattgacaacatttgtttatttcgttttggtaatgtgaacttgctgttttgtattatacttgaattgattcatttgctatttttct--tttgggggtcccaaaatttgattgaattggtgatatagGTTGGATGCGCATCGAATGCTGCAATTGTTGAGAGGGAAACGACTGGTTTTCGTTGGCGATTCGCTCAATAGGAACATGTGGGAGTCATTGATTTGCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtacgtgagtctaataatccaatgatataagtgtgtgtatgaatatatgaaagGTTAAATGGAGGTAAATTGCTTGAGATGATTAGAGGAAGAAGGCTAGTGTTTGTTGGAGATTCGCTGAATAGAAACATGTGGGAGTCTTTGGTTTGCATT
gtctaat putative branch site (score: 3)
tatgaatatatgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattataacacttggtttcttttttttacatggtggtgagtgactggtacgtgagtctaataatccaatgatataagtgtgtgtatgaatatatgaaagGTTAAATGGAGGTAAATTGCTTGAGATGATTAGAGGAAGAAGGCTAGTGTTTGTTGGAGATTCGCTGAATAGAAACATGTGGGAGTCTTTGGTTTGCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT