Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgaaattatgtgtcaagaataaacgtgttaggatattacaattatattgcttatttgcccaactaaaaaagattatgctgcttattgtccttagggagttaggacctgcattttgaaaataatgttctctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16650.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G15170.1 (Glycine max), 3'ss of exon 3
gtaagtgaaattatgtgtcaagaataaacgtgttaggatattacaattatattgcttatttgcccaactaaaaaagattatgctgcttattgtcc-ttagggagttag---gacctgcattttgaaa--ataatgttctctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
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---------------------------------------------------tctctctgtagtctaatgcatataatttttctctttttttctcaattaattaattaaccagttcttcctgtggaaatgacaatcatattcttgtctccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACATTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G41740.1 (Glycine max), 3'ss of exon 3
gtaagtgaaattatgtgtcaagaataaacgtgttaggatattacaattatattgcttatttgcccaactaaaaaagattatgctgcttattgtccttagggagttaggacctgcattttgaaaataatgttctctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
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---------------------------gttctctttcctagt-caggcagatgatttatttattt--ttaaaaataataatgaataatttcttcctgtggaaatgacaatc------------atcatgttcc---tgcacccagATAACAGATGCTGTTGTTGTTGCACGAATTCTTAATGCCACACTAGTAGTACCTGAGTTGGATCATCATTCTTATTGGAAAGATGACAG
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G04720.1 (Glycine max), 3'ss of exon 3
gtaagtgaaattatgtgtcaagaataaacgtgttaggatattacaattatattgcttatttgcccaactaaaaaagattatgctgcttattgtccttagggagttaggacctgcattttgaaaataatgttc-tctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
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----------------------------------------ggaggctcagattctttctgtagtc---taatgaatataatttttctcaat-taattaataaacaagttcttcc--tgtggaaatgacaatcatattcttgtccagATAACAGATGCAGTTGTTGTTGCAAGAATTCTTAATGCTACACTAGTTGTACCTGAGTTGGATCATCAATCTTTTTGGAAAGATGACAG
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G03640.1 (Glycine max), 3'ss of exon 4
gtaagtgaaattatgtgtcaagaataaacgtgttaggatattacaattatattgcttatttgcccaactaaaaaagattatgctgcttattgtccttagggagttaggacctgcattttgaaaataatgttctctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
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-----------------------gttagtttcctagtcaggctca-taattttatatatttttaaaaataaaaatgaacaagttcttt-------ctatggaaatgacactc-----------atcatgttcc---tgcatccagATAACAGATGCTGTTGTTGTTGCCCGAATTCTTAATGCCACACTAGTAGTACCGGAGTTGGATCATCATTCTTATTGGAAGGATGACAG
upper sequence: AT4G16650.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0229g00100.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtgaaa------ttatgtgtcaagaataaacgtgttaggatat-tacaat-------tatattgcttatttgcccaactaaaaaagat----tatgctgcttattgtccttagggagttaggacctgcattttgaaa---ataatgttctctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
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gtaagtataaagattcttctgtagctgctacatgttcattaaaacatatatagtggaaggatatgctgttgccgtgtcaacttcataaacatattataaacttgtttcagttatttacttgtttatcctttttgcatggaatttacaatccatttcctgcactcagATAACCGATGCTGTAGTAGTTGCTCGGATTCTTAATGCTACATTAGTTGTACCAGAGTTGGATCATCATTCCTTCTGGAAAGATGATAGMapped 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|124868723|gb|EH953160.1|EH953160EST: ATATTTGCTTATTGCAGCTAGTGGAGGCCTTAACCAACAAAGAACAGGA ATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTA
genomic: ATATTTGCTTATTGCAGCTAGTGGAGGCCTTAACCAACAAAGAACAGGAgtaagtgaaa ... ttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtccttagggagttaggacctgcattttgaaaataatgttctctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
tgttctcttt CT-rich tract
attttgaaaataatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgaaattatgtgtcaagaataaacgtgttaggatattacaattatattgcttatttgcccaactaaaaaagattatgctgcttattgtccttagggagttaggacctgcattttgaaaataatgttctctttgtgtgcagATAACTGATGCAGTGGTTGTTGCACGGATTCTTAATGCTACTTTAGTTGTACCCGAGTTGGATCACCATTCTTACTGGAAAGATGACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG