Sequence
atgc intronic sequence ATGC exonic sequenceTGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctctag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13470.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 11
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgct---cttactgcattt-tcaactatttcccatctctag--------------------
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TGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAACAGAAGgtaggaaaacaaatgaaataatctttggttattgtttcatttcatcctaggttcaaggcatttgttttctattgtcaataattaaaatttctttttggcttcaag
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 11
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtg-attggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctctag-------------------------------------------------------------------------------------------
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TGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTCTGAGACTGGCAGCTAGAGTTGACGCCATCAAGGACAACCTGGAGAATGATGAGCAGAAGgtttacaaccatgatctactttattcattgtttttgttcgagtgttctataaacctcatctctcaaaagttctgtttttgtgcctgctactatgtatatgggttagaaatgaccatctcgaatttgttgtcctttctaattgacttgttgtatgtattgcttgaactttttag
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 5
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaatt--ttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccat-ctctag-----------
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TGTTGAGGAAGGTATTGTTGTTGGTGGAGGATGCACCCTTTTGCGGCTTGCAGCTAAAGTCGATGCCATCAAGGATACACTGGAGAACGATGAGCAGAAGgtaag-aacaaaatctgtgattgattaaaaagagtagactacagagcagccttgttataggttcgagtataactgacacgctgaagtaccattag
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G083716_T03 (Zea mays), 5'ss of exon 10
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattt-tttgcaa---------------attgcttgctcttactgcattttcaactatttcccatctctag------------
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CGTTGAGGAAGGTATTGTTGTTGGTGGAGGGTGCACTCTTTTGCGGCTTGCAGCTAAAGTCGACGCCATCAAGGATACACTGGAGAACGACGAGCAGAAGgtaaa-aacaaaatctgcaatcccgtaattcatttgaaagaggatggaggcaacagagcacaaccttgctataggttcaactatggctgacattctgaactgacattag
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggc------aaaatcaagaattttgaaattttttgcaaattgc----ttgctcttactgcattttcaactat-ttcccatctctag----------------------------------------------------------
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TGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcag
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA08G18760.3 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattgg------caaaatcaagaattttgaaattttttgcaaattgc----ttgctcttactgcattttcaactat-ttcccatctctag-----------------------------------------------------------------
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----GAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAGTGAgtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcaggttggag
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggc------aaaatcaagaattttgaaattttttgcaaattgct-tgctcttact----gcattttcaactatttcccatctctag--------------------------------------------------------
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TGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGACACAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatacaagtttcttggatgttgtgatatttttgttttgggtgctgggaaatgcttctgactgttgctttcaactcaactcctagcgtggtcatgacttcaaaattgtgtttaattgttgcag
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 11
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttc--ccatctctag---------------------------------------------------------------------------
|||||||||||| ||||| || |||||||| |||||||| || | ||||| |||||||| |||||||||||||| || ||||| |||||||| ||||||||||| | | ||| | ||| |||| || | || ||| ||| ||| |
TGTTGAGGAAGGGATTGTTGTAGGTGGTGGGTGCACTCTCCTGAGACTTGCCTCAAAGGTGGATGCCATCAAGGACACGCTTGATAATGATGAGGAAAAGgtgatacttgtggctgtgttcaatatgggatttgtccaataccttgagttt-tggttttcccaatagtttgaatcatgctgaatgtgttcaaaatgtgtcaatatattggccaggatatagtgtttatcctcttaaagtggacttgaattgattgcag
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 10
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctctag
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TGTTGAAGAAGGCATCGTTGTCGGTGGGGGAATTGCTCTTCTAAGACTGTCTAGCAAGGTTGATGCCATCAAGGATACCCTTGAGAATGACGAGCAAAAGgtga--ggccacttcagaaagcttt---ccctctgaaagtcaattacctgtttcag-------------------------
upper sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ33580 (Selaginella moellendorffii), 5'ss of exon 10
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaa-ttttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctctag
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TGTTGAAGAAGGCATCGTTGTCGGTGGGGGAATTGCTCTTCTAAGACTGTCTAGCAAGGTTGATGCCATCAAGGATACCCTTGAGAATGACGAGCAAAAGgtga--ggccacttcagaaagctttgaccctccctctgaaagtcaagtacctgtttcag-----------------------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|125261013|gb|EL275098.1|EL275098EST: ACCCTTGAAAATGATGAAGAAAAG GTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATA
genomic: ACCCTTGAAAATGATGAAGAAAAGgtgattggca ... ccatctctagGTTGGAGCGGAAATTGTTAAAAGAGCACTGAGTTACCCTCTGAAATTGATA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgctcttactgcattttcaactatttcccatctctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA