Sequence
atgc intronic sequence ATGC exonic sequenceGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22140.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g32620.2 (Oryza sativa), 5'ss of exon 2
-------------------------------GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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TGCTTGTGTTTTCTTTTTCGTTTTTCTGAAGATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattccattaataaaccgcctctgttatgatgcatttcagtctatatagtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat-----------------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattccattaataaaccgcctctgttatgatgcatttcagtctatatagtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat-----------------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G091265_T03 (Zea mays), 5'ss of exon 2
-------------------------------GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaa-tgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagacta-tatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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TGATCTTATGTGACATTGTTTGTATGTGAAGATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtgaaatggctccacattttgccc-------------------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G091265_T05 (Zea mays), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaa-tgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagacta-tatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtgaaatggctccacattttgccc-------------------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G091265_T01 (Zea mays), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaa-tgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagacta-tatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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----------TGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtgaaatggctccacattttgccc-------------------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G119357_T01 (Zea mays), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
||| ||||||||||| ||||| ||||| || || || |||||||||||||| |||| ||||| |||||||| |||||||| | | | || | | || ||||| ||| || || | || | || ||| ||| | || | | || | || | |
GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgta--------catttgtctc----aatgattttca-atttacatttcactga---------tatttgcctttgttcagtctattttatgcttctacaa-agcaaatgctttaaatctctgga------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttat-tctgatttactttgtttggagtttggattttgttta---------tgtatgtggaatttgagaaatagatgttatttactgggttgaagggat-------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G20180.1 (Glycine max), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtgtat-tctgctttactttgttgtgttattgtgtttgga--gtttggattttgcttatttaggtgtttgtttatgtatgt-------ggaatt--tgagaa-----------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactata--tgtctg-tttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaa-accagtatat-tctgctttttt---ttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaattttagcattagatgc-----gttgtt----------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G35680.2 (Glycine max), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaa--tgttgatatttgtcttttttattaact-tccttacttgtgttt-caacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
||| ||||| || || |||||||| || ||||| || ||||||||||||||||| || ||||| || ||||||| || | || || ||| || ||| | |||| | ||| | | | ||| ||||| ||| | | ||
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaaagccagtgtattctgctttctttgtttactgttattacatttgtgagtggtttttggatgtccgggtctctaattttagcattagatgcgttgttt---------------------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S56_182V6.1 (Physcomitrella patens), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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TTATTGCAAGTGTGAAATGCCATACAATCCTGACGACTTGATGGTTCAATGTGAAATCTGCAAAGACTGgttg--gtctatattcctcctttctatgcaagtgca---gtggattattgtagaagtt-gtttttatctcagtatttt--cctgaatattcgcaaggtgaacttaccc---------------------------
upper sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
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GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaag---ccttggcagcctccgatgaaaaaaatggcag-----------------------------------------------------------------------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|164189621|gb|ES019576.1|ES019576EST: TGGTGCAGTGTGAAGGCTGCAAAGACTG GTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGA
genomic: TGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttg ... gctgttgtagGTATCATCCTGCGTGTGTTGGCATGACGATTGAAGAAGCAAAGAAGCTTGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG