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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGAAGCCAAGCTTTTCGTCGGAAATTTGGCTTATGATGTTAATAGCCAAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttagctgctttcttcttgtgctcatatggtcgtcttgatgcgtttatatgttgttcattatgcattgcttaaggttatttatgtgtgttttgtg...

Basic information

species Arabidopsis thaliana
transcript AT4G24770.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA04G36420.2 (Glycine max), 5'ss of exon 1
GGAAGAAGCCAAGCTTTTCGTCGGAAATTTGGCTTATGATGTTAATAGCCAAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtga-----------atttagctgctttcttcttgtgctcatatggtcgtcttgatgcgt-ttatatgttgttcattatgcattg----cttaaggtta-tttatg-tgtgttttgtg
|||||| || ||||| ||||| || || ||| |||| || ||| |||||||    ||||| |||||||| || |||||||| || ||||||||||||||||| |           |   ||      ||||    | ||| | |     | |  ||   | ||| || || ||   |  |  |||    ||| |  | |   | || |||| |||  |
GGAAGAGGCAAAGCTCTTCGTTGGGAACTTGCCTTACGACGTTGATAGCCAGAAATTGGCCATGCTCTTCGAACAAGCCGGAACCGTTGAAATCGCCGAGgtcagagagagagagagagagagaggctctttaccttctcgtgtttcaatttgaatttctgttaaatattattttgttagggttggaaacttgaaatgaacgtgtggtgtggttttag
















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|124714026|gb|EH805428.1|EH805428
EST:     TTGAGCAAGCCGGTAACTGTTGAAATCGCCGAG                         GTTATATACAATAGGGAAACTG
genomic: TTGAGCAAGCCGGT-ACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTG
EST: gi|125033440|gb|EL105709.1|EL105709
EST:     AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAG                         GTTATATACAATA
genomic: AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATA
EST: gi|125008774|gb|EL081043.1|EL081043
EST:     AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAG                         GTTATATACAATAGGGAAA
genomic: AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAA
EST: gi|124962681|gb|EL037067.1|EL037067
EST:     AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAG                         GTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
genomic: AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
EST: gi|125060500|gb|EL129177.1|EL129177
EST:     AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACAGTTGAAATCGCCGAG                         GTTATATACAATAGGGAAACTGACCAGAGTCGTGGG
genomic: AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTGACCAGAGTCGTGGG
EST: gi|125037554|gb|EL109823.1|EL109823
EST:     GAAATCGCCGAG                         GTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
genomic: GAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
EST: gi|86087405|gb|DR383164.1|DR383164
EST:     AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAG                         GTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
genomic: AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
EST: gi|125323686|gb|EL337768.1|EL337768
EST:     AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAG                         GTTATATACAATAGGGAAACTGA
genomic: AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTGA
EST: gi|124818471|gb|EH903337.1|EH903337
EST:     AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAG                         GTTATATACAATAGGGAAACTGA
genomic: AAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTGA
EST: gi|125062857|gb|EL131051.1|EL131051
EST:     ACTGTTGAAATCGCCGAG                         GTTATATACAATAGGGGAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
genomic: ACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
EST: gi|124942368|gb|EL018641.1|EL018641
EST:     CTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAG                         GTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
genomic: CTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAATAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGACA
EST: gi|124797272|gb|EH886951.1|EH886951
EST:     CTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAG                         GTTATATACAATTAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGAC
genomic: CTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttag ... tggttgtaagGTTATATACAA-TAGGGAAACTGACCAGAGTCGTGGGTTTGGATTTGTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGAAGCCAAGCTTTTCGTCGGAAATTTGGCTTATGATGTTAATAGCCAAGCTTTGGCTATGCTCTTTGAGCAAGCCGGTACTGTTGAAATCGCCGAGgtgaatttagctgctttcttcttgtgctcatatggtcgtcttgatgcgtttatatgttgttcattatgcattgcttaaggttatttatgtgtgttttgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttcttc