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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCTTTCCAACAACAAGATAAATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagcatccataagacctccagttttattgtttatttctagcaaaagatgaaaatggtttgtgaactcttgcattcttgttatag

Basic information

species Arabidopsis thaliana
transcript AT2G26330.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G26330.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA14G11220.2 (Glycine max), 5'ss of exon 18
GGATCTTTCCAACAACAAGATAAATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagc-atcca-----taagacctccagtttt-attgtttatttctagcaaaagatgaaaatggtttgtgaactcttgcattcttgttatag
|||| |||| ||||| ||  ||  |||   ||| ||||||||||||||||| ||||| |||||||| ||| ||||||  |||       | | || |  | | |  |   | | ||  |    |||| | | | |  ||| |    | ||               
GGATATTTCAAACAATAAATTAGTTGGTTCCATCCCTTCTTCCCTTGGTGACTTGGAACATCTTCTGAAGTTgtgagttatctgcttagtcatacttagaatctggaccatgtcttcttgctgaaagctaatattcatttatt--ttgttag-------------

upper sequence: AT2G26330.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA17G34380.1 (Glycine max), 5'ss of exon 19
GGATCTTTCCAACAACAAGATAAATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagc-atcca-----taagacctccagtttt-attgtttatttctagcaaaagatgaaaatggtttgtgaactcttgcattcttgttatag
|||| |||| ||||| ||  ||  |||   ||| ||||||||||||||||| ||||| |||||||| ||| ||||||  |||       | |  | |  | | |  | | ||| ||  ||   |||| | | | |  ||| |    | ||               
GGATATTTCAAACAATAACTTAGTTGGTTCCATCCCTTCTTCCCTTGGTGACTTGGAACATCTTCTGAAGTTgtgagttatctgcctagtcatgcttagaatctggactatttcttcttactgaaagctaatattcatttatt--ttgttag-------------

upper sequence: AT2G26330.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA04G05910.1 (Glycine max), 5'ss of exon 9
GGATCTTTCCAACAACAAGATAAATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagcatccataagacctccagttttattgtttatttctagcaaaagatgaaaatggtttgtgaactcttgcattcttgtta-tag
|||| | || || || || |||| |||    |||||||||||| ||||||| ||||| |||||||| ||| ||||||  |   ||||    | ||||  | | || |  | |||      |||  | | |||  |||   || | | || | ||  |||
GGATATATCAAATAATAATATAATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTTgtgagtcttt-taag----ctagtt--acttttgaaatttag-----aatgttactagttactgattgctagtaatcattttgctag

upper sequence: AT2G26330.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA06G05900.1 (Glycine max), 5'ss of exon 19
GGATCTTTCCAACAACAAGATAAATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagcatccataagacctccagttttattgtttatttctagcaaaagatgaaaatggtttgtgaactcttgcattcttgtta-tag
|||| | || || || || |||| |||    |||||||||||| ||||||| ||||| |||||||| ||| ||||||  |   |   |     ||||  | | || |  |||||      |||  | |  ||  |||   || | | || | ||  |||
GGATATATCAAATAATAATATAATTGGTTCTATTCCTTCTTCCATTGGTGACTTGGAACATCTTCTGAAGTTgtgagtttttttggca-----agtt--acttttgaaatctag-----aatgttacttcttactgattgctagtaatcattttgctag

upper sequence: AT2G26330.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 5'ss of exon 18
GGATCTTTCCAACAACAAGATAAATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagcatccataagacctccagttttattgtttatttctagcaaaagatgaaaatggtttgtgaactcttgcattcttgttatag
|||  |||| || |||| ||| | |||   |||||||||||||||||| || |||||||||||||| ||  ||| |   |||| |        || |   ||  |  ||||   ||||   |     | | |  | | || ||   ||||||   |||
GGACATTTCAAATAACAGGATTACTGGCTCCATTCCTTCTTCCCTTGGAGACTTGGAGCATCTTCTAAAACTgtaa-tttccacag-----ttagctaccttcctgttttc---caaagttttcttcttgctgat-atctttttttttcttgggttag

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|164034803|gb|ES024009.1|ES024009
EST:     GAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGAT                         GAACTTGAGTAGAAATCATATAACCGGTGTAGTTCCAGGCGACTTTGGAAA
genomic: GAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagcatcc ... cttgttatagGAACTTGAGTAGAAATCATATAACTGGTGTAGTTCCAGGCGACTTTGGAAA
EST: gi|124882377|gb|EH961279.1|EH961279
EST:     AATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGAT                         GAACTTGAGTAGAAATCATATAACTGGTGTAGTTCCAGGCGACTTTGGAA
genomic: AATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagcatcc ... cttgttatagGAACTTGAGTAGAAATCATATAACTGGTGTAGTTCCAGGCGACTTTGGAA
EST: gi|86067492|gb|DR363249.1|DR363249
EST:     AATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGAT                         GAACTTGAGTAGAAATCATATAACCGGTGTAGTTCCAGGCGACTTTGGAAA
genomic: AATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagcatcc ... cttgttatagGAACTTGAGTAGAAATCATATAACTGGTGTAGTTCCAGGCGACTTTGGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCTTTCCAACAACAAGATAAATGGAATCATTCCTTCTTCCCTTGGTGATTTGGAGCATCTTCTCAAGATgtgagcatccataagacctccagttttattgtttatttctagcaaaagatgaaaatggtttgtgaactcttgcattcttgttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA