Sequence
atgc intronic sequence ATGC exonic sequencegtaagctgcttgctaaaaccattcaccattttaatgcatctcttaaacaacaacttcaaaactcatgttctaatcaattgttccagGCTGTTCCTCCTGTAATCCACAGAGATATCAAATCTTCCAACATCTTGCTGGATCAATCTATGAGAGCTCGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54590.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G41510.1 (Glycine max), 3'ss of exon 5
gtaagctgcttgctaaaaccattcaccattttaatgcatctcttaaacaacaacttcaaaactcatgttctaatcaattgttccagGCTGTTCCTCCTGTAATCCACAGAGATATCAAATCTTCCAACATCTTGCTGGATCAATCTATGAGAGCTCGG
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gtaagtttcca--tgagatc-tgcacatatttaat-tatactttgtatgtatattgttaattatatgtactt-----tcacttcagGCAGTTCCTCCTGTAATCCATCGAGATATCAAATCTTCCAATATTCTGTTGGATCAATCCATGAGAGCCAGG
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G16650.1 (Glycine max), 3'ss of exon 4
gtaagctgcttgctaaaaccattcaccattttaatgcatctcttaaacaacaacttcaaaactcatgttctaatcaattgttccagGCTGTTCCTCCTGTAATCCACAGAGATATCAAATCTTCCAACATCTTGCTGGATCAATCTATGAGAGCTCGG
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gtaagtt---tacatgtgatttgcaacaatttaattttactttgtatgtatattgttataa----tagtatgtattgtcacttcagGCAGTTCCTCCTGTAATCCATCGAGATATCAAATCTTCCAACATTCTGTTGGATCAATCCATGCTAGCCAGG
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G34410.1 (Glycine max), 3'ss of exon 5
gtaagctgcttgctaaaaccattcaccattttaatgcatctcttaaacaacaacttcaaaactcatgttctaatcaattgttccagGCTGTTCCTCCTGTAATCCACAGAGATATCAAATCTTCCAACATCTTGCTGGATCAATCTATGAGAGCTCGG
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gtaag-tgttcatgtgatcta--cactgagataattctgctttct-----ctatttagttataactgtatttgttgac-actccagGCAGTTCCTCCTGTAATCCATCGAGATATCAAATCTTCTAACATTCTCTTGGACCAGTCCATGCGAGCCAGG
upper sequence: AT5G54590.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G36140.2 (Glycine max), 3'ss of exon 5
gtaagctgcttgctaa--aaccattcaccattttaatgcatctcttaaacaacaacttcaaaactcatgttctaatcaattgttccagGCTGTTCCTCCTGTAATCCACAGAGATATCAAATCTTCCAACATCTTGCTGGATCAATCTATGAGAGCTCGG
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gtaagtgtcccgtgaactaaactgagataattctgctttctctatttagttataa-----------atgtatttgttgac-acttcagGCAGTTCCTCCCGTAATCCATCGAGATATCAAATCTTCTAACATTCTCTTGGACCAGTCCATGCGAGCCAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgcatctcttaaacaacaacttcaaaactcatgttctaatcaattgttccagGCTGTTCCTCCTGTAATCCACAGAGATATCAAATCTTCCAACATCTTGCTGGATCAATCTATGAGAGCTCGG
ttctaat putative branch site (score: 2)
ttgttcc putative PPT
taatcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctgcttgctaaaaccattcaccattttaatgcatctcttaaacaacaacttcaaaactcatgttctaatcaattgttccagGCTGTTCCTCCTGTAATCCACAGAGATATCAAATCTTCCAACATCTTGCTGGATCAATCTATGAGAGCTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT