Sequence
atgc intronic sequence ATGC exonic sequenceTATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgtaacatattttttcatacaattttgagaacctgcataattcattacataatgtttcttgttctattttgatttgtgcatctgataagctttgaagaagt...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G53620.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 6
TATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgtaacatattttttcataca-attttgagaacctgcataattcattacat-aatgtttcttgttctattttgatttgtgcatctgataagctttgaagaagt
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TGTGCTGTATTCATCAGTTGTTTACCCTCACAACTATGGATTCATTCCTCGCACGCTTTGTGAAGACAGTGATCCTTTGGATGTACTGGTTATAATGCAGgtatgcttcttttttatatatatcattgggattcacaaaat--ggtacatcagtagtgatctgagtatccttgggcataagttgagctaattttcaaatctt
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 5
TATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgtaacatattttttcatacaattttgagaacctgcataatt--cattacataatgtttcttgttctattttgatttgtgcatctgataagctttgaagaagt
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TATACTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTTATTCCACGTACTATTTGTGAGGACGGTGATCCCATGGATGTCTTGGTTATTATGCAGgtacttgaatattgttcatattgccaacttcttgc-tagttagtgtgattcaagttttctgaaaatggattgtgtaataagtc-aacaacttccgttcaact
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 7
TATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgta---acatattttttcatacaattttgagaacctgcataattcatta--cataatgtttcttgttctattttgatttgtgc---atctgataagctttgaagaagt
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CGTGCTTTACTCATCAGTTGTTTATCCTCACAACTATGGGTTTATCCCTCGTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatatatccgttcatattatcaaattttcct-tgtaaatcagtgggcatcgtgtatatatttaaaaatgagattactttcaaactgacaaactttc-------
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G33000.4 (Glycine max), 5'ss of exon 7
TATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgta---acatattttttcatacaattttgagaacctgcataattcattacataatgttt-cttgttctattttgatt-tgtgcatctgataagctttgaagaagt
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TGTTCTTTACTCATCAGTTGTGTATCCTCACAATTATGGGTTTATCCCACGTACTATTTGTGAGGACAGTGATCCCCTGGATGTCTTGATTATTATGCAGgtatttatatatccgttgatata---tcaaattttccccggatgtcttcaataagacatgcatgcattcttacgattgtctgcatctcattttttttgtctac--
upper sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 5'ss of exon 6
TATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgtaacat---attttttcatacaattttgagaacctgcataattcattacataatgtttcttgttctattttgatttgtgcatctgataagctttgaagaagt
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TATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCATTATGCAGgtactattcaagacttttttttttccttactaaatttcaacatttgt-attttgtgaatga-gatagactgagatttttatagcaaaggtaaatgcacgtaa-Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125160838|gb|EL188236.1|EL188236EST: GTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCNG GA-CCGGTGATCCCAGGATGCTTTCTTCGGGCCAAA
genomic: GTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgtaacatatt ... ttttctacagGAACCGGTGATCCCAGGATGCTTTCTTCGGGCCAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TATTCTTTACTCATCTGTCGTATACCCACACAACTATGGGTTCATTCCGCGTACCCTTTGTGAGGACAGTGACCCTATTGATGTTCTTGTCATTATGCAGgtaacatattttttcatacaattttgagaacctgcataattcattacataatgtttcttgttctattttgatttgtgcatctgataagctttgaagaagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaag