Sequence
atgc intronic sequence ATGC exonic sequenceTAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52520.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os07g07060.1 (Oryza sativa), 5'ss of exon 3
TAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcag------------------------
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AAGATGGGAAATGAGGACTAAGCCATTCATCAGAACTCTTGAATTTCTATGGCAAGAAGGTCATACAGCTCATGCCACCCTTGAAGAGGCAGAAAAGGAGgtttgttgaatgctaatcattgcacaagttccttc-atgcacttgataacacaaattggaaagaatggaagattctaatgtaatatcatctgctccatttttctcttcag
upper sequence: AT5G52520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G107089_T01 (Zea mays), 5'ss of exon 5
TAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctc---------tatagagctgtggtcaact-tgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcag------------------------------------------------------
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AAGATGGGAAATGCGGACTAAACCATTCATCCGAACTCTTGAATTTTTATGGCAAGAAGGCCATACAGCCCATGCCACCCTTGAGGAGGCAGAGAAGGAGgttagttttcacattttctttccaaattattgttgcttctgctgaaatttcaaagccatgcatgtgatggtgcaggaaagtcatttcttgataaacaatgaaagattctagtgcactacctcatattctccaattgttattgctctgcag
upper sequence: AT5G52520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA09G24670.1 (Glycine max), 5'ss of exon 5
TAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgatta-gttttgt---attgcag
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AAGATGGGAGATGCGCACCAAACCATTTGTGAGAACTCTTGAATTTCTTTGGCAAGAAGGACATACTGCTCATGCAACTCCAGAGGAGGCCGAAAAAGAGgtgcacatctttt-------ctgtcaagatgacaaaatctttactagtgtagttgcataatcttagtgacaatattctgttcaactgcag
upper sequence: AT5G52520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA16G29890.1 (Glycine max), 5'ss of exon 5
TAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgatta-gttttgt---attgcag
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AAGATGGGAGATGCGCACTAAACCATTTGTGAGAACTCTTGAATTTCTTTGGCAAGAAGGACATACTGCTCATGCAACTCCAGAAGAGGCAGAAAAAGAGgtccacttctttt-------ctgtcaagatg-ataaatctttactagtataattgcataatcttagtgacgacattctgttcaactgcag
upper sequence: AT5G52520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv16s0050g00960.t01 (Vitis vinifera), 5'ss of exon 5
TAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcag
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GAGATGGGAGATGCGGACAAAACCATTTGTGAGGACTCTTGAATTTCTCTGGCAAGAGGGCCACACTGCTCATGCCACCCCTGAAGAGGCAGAAAAAGAGgtattcatgatatctatctgaaaaccactccta---atctttcttatgttttcttgtctt--catttaacagattgtaaactgcagMapped 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|116443936|gb|EG486528.1|EG486528EST: GGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAG GCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCA
genomic: GGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctc ... tgtattgcagGCGAAACAGATGATCGAGATCTACACCAGATTTGCTTTTGAGCAAACTGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TAGATGGGAAATGCGGACGAAACCATTTATTAGGACTCTTGAATTTCTATGGCAAGAGGGTCATACTGCTCATGCCACTCCTGAGGAGGCAGAAAAGGAGgtttgttctctatagagctgtggtcaacttgtggagattttttttgtggtactctcctgtgacaaatgattagttttgtattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG