Sequence
atgc intronic sequence ATGC exonic sequenceACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgtcttgatatatttgttactttcccgcatgtcattgtagtgaatgtagtccttgggaagagtcacattataagagtcctcaatttatattcac...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G01310.2 |
intron # | 16 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA13G05060.1 (Glycine max), 5'ss of exon 17
ACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgtcttgat-atatttgttactttcccgcatgtcattgtagtgaatgtagtccttgggaagagtcacattataagagtcctcaatttatattcac-
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ACCAGATCGAGAAAGCGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCGTCAAGTTAAAGCAGTTCTTGAGGAGgttattaattctcttgacactgttttttctatgatatgaatatgttttgtattatgaacctactagtaattgaaatttgaaaat--taaatttccttgtatc
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA19G02260.1 (Glycine max), 5'ss of exon 13
ACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgt-cttgatatatttgttacttt--cccgcatgtcattgtagtgaatgtagtccttgggaagagtcacattataagagtcctcaatttatattcac
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ACCAGATCGAGAAAGTGATAGTGAGGCTGAAGATGTTGAGCATGCTGAAAAGCTTCATCAAGTTAAAGCAGTTCTTGAGGAGgttattaattctcgacactgttttttctatgatactcatgagtatgttttgtattatgaacctactagtaattgaaatttgaaaat--taaatttcttttta-
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA09G37610.1 (Glycine max), 5'ss of exon 13
ACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgtcttgatatatttgttactttcccgcatgtcattgtagtgaatgtagtccttgggaagagtcacattataa---gagtcctcaatttatattcac---
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ACCAGATCGAGAAAGTGATAGTGAGGCTGAAG---TCGAGCACGCTGAAAAGCTCCGTCAAGTTAAAGCTGTCCTTGAAGAGgtttttaattttcttaactttgttcatt------atatgataatagcaagtttgtagtgtattaataacctgatggtaatttaaatttgaaatttatatttctgtg
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA18G49000.1 (Glycine max), 5'ss of exon 15
ACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgtcttga-tatatttgttactttcccgcatgtcattgtagtgaatgtagtccttgggaagagtcacattataagagtcctcaatttatattcac---
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ACCAGATCGAGAAAGTGATAGTGAGGCTGAAG---TCGAGCACACTGAAAAGCTCCGTCAAGTTAAAGCTGTCCTTGAAGAGgtttttaatttcaactttgttcattatatgataata-gcaagtttgtagagtattaacctgatggtaactgaaacttgaaatttac---atttctgtggactgt
upper sequence: AT3G01310.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 5'ss of exon 15
ACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgtcttgatatatttgttactttcccgcatgtcattgtagtgaatgtagtccttgggaagagtcacattataagagtcctcaatttatattcac--------
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ACCTGGTCGAGAAAGTGACAGTGAAGCAGAAGATCTTGAGCATGCTGAAAAACTTCGTCAAGTTAAAGCAGTCCTTGAAGAGgtcacttgtttagtttctcttgaaatt-------atgtgatttcttgaaatcatgcctttttttttcttttttctattattattttca-tctatagtgataagtggttMapped 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|19874907|gb|AU235738.1|AU235738EST: ACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAG GGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAG
genomic: ACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgtc ... tgatatgcagGGAGGACATTTCTCTGGTATATACAGGAAGGTTCAACTGAAGCCGCTGAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACCAGGTCGTGAAAGTGATAGTGATGCAGAAGACCTTGAACATGCTGAGAAGCTTCGGCAAGTTAAAGCAGTCCTTGAAGAGgttaggtgtcttgatatatttgttactttcccgcatgtcattgtagtgaatgtagtccttgggaagagtcacattataagagtcctcaatttatattcac
- - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttcccg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaagag