Sequence
atgc intronic sequence ATGC exonic sequencegtatgaccgtggagagatatctttcaaatgttcttgttcttttaggctaagaaacattgaccatgaatttagtcactataatagtgcaattttctggcagGTGATGGTGACAGAAATATGGTTTTAGGAAACAAATTCTTTGTCACTCCTTCAGACTCTGTAGCTATCATCGCAGCCAATGCACAAGAAGCAATTCCATA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51820.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 13
gtatgaccgtggagagatatctttcaaatgttcttgttcttttaggctaag--aaacattgaccatgaatttagtcactataa--tagtgcaattttctggcagGTGATGGTGACAGAAATATGGTTTTAGGAAACAAATTCTTTGTCACTCCTTCAGACTCTGTAGCTATCATCGCAGCCAATGCACAAGAAGCAATTCCATA
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---ttattgcaga-agatgtggttgatgtatgccagtgtaacaatgttttgttagtctgtgtttgtttatttgatgatgttcatgtatttcaatctttgttcagGGGATGGTGATAGAAATATGATTTTAGGAAGAAGTTTCTTTGTAACTCCTTCAGACTCTGTAGCAGTTATTGCAGCCAATGCAAGAGAAGCGATTCCATA
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 13
gtatgaccgtg-gagagatatctttcaaatgttcttgttcttttaggctaagaaacattgaccatga--atttagtcactataa--tagtgcaattttctggcagGTGATGGTGACAGAAATATGGTTTTAGGAAACAAATTCTTTGTCACTCCTTCAGACTCTGTAGCTATCATCGCAGCCAATGCACAAGAAGCAATTCCATA
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-----attgcataagatgtggttgatgtatgcttgtgtaacattgttttgtctgcctttgtgtgtgtttattcgatgatgttcatgtatttcaatctttgttcagGGGATGGTGATAGAAATATGATTTTAGGAAGAAGTTTCTTTGTAACTCCTTCAGACTCGGTAGCAGTTATTGCAGCCAATGCAAGAGAAGCGGTTCCATA
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ34621 (Selaginella moellendorffii), 3'ss of exon 12
gtatgaccgtggagagatatctttcaaatgttcttgttcttttaggctaagaaacattgaccatgaatttagtcactataatagtgcaattttctggcagGTGATGGTGACAGAAATATGGTTTTAGGAAACAAATTCTTTGTCACTCCTTCAGACTCTGTAGCTATCATCGCAGCCAATGCACAAGAAGCAATTCCATA
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------------------------------------gtaaagcagagttaaaaac-tttactgcgagcggattttttg----aattcaaaaagaatgcagGTGATGGAGACCGGAACATGATCCTAGGCAACAATTTCTTTGTCACTCCTTCGGACTCTGTTGCCATGATTGCAGCCAATGCTCAGCCATGCATTCCATA
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: EFJ32824 (Selaginella moellendorffii), 3'ss of exon 12
gtatgaccgtggagagatatctttcaaatgttcttgttcttttaggctaag--aaacattgaccatgaatttagtcactataatagtgcaattttctggcagGTGATGGTGACAGAAATATGGTTTTAGGAAACAAATTCTTTGTCACTCCTTCAGACTCTGTAGCTATCATCGCAGCCAATGCACAAGAAGCAATTCCATA
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----------------------------------------gtaaagcagagttaaaactttattgcgagcggattttttgaattcataaagcat----gcagGTGATGGAGACCGGAACATGATCCTAGGCAACAATTTCTTTGTCACTCCTTCGGACTCTGTTGCCATGATTGCAGCCAATGCTCAGCCATGCATTCCATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctaagaaacattgaccatgaatttagtcactataatagtgcaattttctggcagGTGATGGTGACAGAAATATGGTTTTAGGAAACAAATTCTTTGTCACTCCTTCAGACTCTGTAGCTATCATCGCAGCCAATGCACAAGAAGCAATTCCATA
cattgac putative branch site (score: 3)
ttttct putative PPT
atgaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaccgtggagagatatctttcaaatgttcttgttcttttaggctaagaaacattgaccatgaatttagtcactataatagtgcaattttctggcagGTGATGGTGACAGAAATATGGTTTTAGGAAACAAATTCTTTGTCACTCCTTCAGACTCTGTAGCTATCATCGCAGCCAATGCACAAGAAGCAATTCCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA