Sequence
atgc intronic sequence ATGC exonic sequenceCAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55990.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G44580.1 (Glycine max), 5'ss of exon 8
CAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcag
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CAGATACAAAGCATGATGGCAAGATTGACAAGGAAGAGTGGAGAAACCTTGTTTTGCGCCATCCGTCACTTTTGAAGAACATGACCCTTCAATATCTCAAgtaattctttaat--taatatttttctagtcaatttctgcggtactctcccaagtggagataaccaaataactgttctttattttaaaaaaaaaatggatga--------------------------------
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G00830.1 (Glycine max), 5'ss of exon 8
CAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcag
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CTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTCTTCAATATCTCAAgtgagtt-----tctttccattacta--accactatttggattttgaaattatcttgcgagggaaatgtaaccaagct-tatt-tgaatgtgttaaaatgaa--tcataat-----------------------
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA07G39940.1 (Glycine max), 5'ss of exon 8
CAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataa-aggtcgtgatcctgttgtgtgcttgctctgcag
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CTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTACAGCATCCATCCCTTCTGAAAAATATGACTCTTCAGTATCTCAAgtgagtt-----tctttccgttaata--accacaatttggattttgaaattgtctggtaagtgagggaaatgttaccaagcttatttg-gatgtgttaaaatgagtca---------------------------
upper sequence: AT5G55990.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 5'ss of exon 7
CAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttccaaatctttctatttatataaccaggattgaatctattca--accaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcag
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CTGACACAAAACATGATGGAAAGATTGACAAAGAAGAGTGGAGAAGCCTTGTTCTACGACACCCATCCCTTTTGAAGAATATGACTCTTCAATACCTCAAgtaagttgtgaat-ttaatgctagtttattttgtttcaactttgatcaggactagcatttttaaatgggaaaatttacacttataccccctga-acctgtca----------------------------------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|124815281|gb|EH900147.1|EH900147EST: GTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAA GGATATCACGACTACGTTTCCAAGCTTTG
genomic: GTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttcca ... tgctctgcagGGATATCACGACTACGTTTCCAAGCTTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGACACAAAACACGATGGAAAGATCGATAAGGAAGAGTGGAGAAGCCTTGTTCTTAGACATCCCAGCCTTCTGAAGAACATGACTCTTCAATATCTCAAgtgagttccaaatctttctatttatataaccaggattgaatctattcaaccaaattccttctctggtttctctttcttctattctccatgatatgtaataaaggtcgtgatcctgttgtgtgcttgctctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC