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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAACCTGGAACTCAGCCTCCTCTTTGCCGTTCTGATAATGACCCTGATGCTGTGTGGGGCGTAAACATGGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttcaagcttcttctcgcttttcaataacagcgtatatttcctctgaactcttttttggggttgtcttag

Basic information

species Arabidopsis thaliana
transcript AT4G14360.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA20G35120.4 (Glycine max), 5'ss of exon 5
AGAGAACCTGGAACTCAGCCTCCTCTTTGCCGTTCTGATAATGACCCTGATGCTGTGTGGGGCGTAAACATGGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttcaagcttct-------------tctcgcttttca---ataacagcg-tatatttcctctgaactcttttttggggttgtcttag-------
||||||||||| | ||  |||||||||||||  |||||| ||||||| |||||  | ||||| ||||| |||||||| ||||| ||  |||||||||| ||| |||   |     |||             | | || || ||   || | || | | | ||| |    | |  |   |||  | |   ||||       
AGAGAACCTGGTAGTCGCCCTCCTCTTTGCCAGTCTGATGATGACCCAGATGCAATTTGGGGAGTAAATATGGAAGCATGCATAACACCTTACAGTGATCgtgagtacccttttctctgtcatttgatggtttttgcattccatggattatagtgatgtctttgcaagtatcaatgccttgttgcttctttagtggcatg

upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G00880.2 (Glycine max), 5'ss of exon 5
AGAGAACCTGGAACTCAGCCTCCTCTTTGCCGTTCTGATAATGACCCTGATGCTGTGTGGGGCGTAAACATGGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttcaagcttcttctcgcttttcaataacagcgtat-atttcctctgaactcttttttggggttgtcttag----------------------------
|||||||| || ||||  |||||||||||||  |||||| ||||||| |||||  | ||||| || || |||||||||||||| ||  |||||  ||||||| |||     | |||  |||    |   |   | |  || | ||  | | || ||| | |||    | | | |                               
AGAGAACCCGGCACTCGCCCTCCTCTTTGCCAGTCTGATGATGACCCAGATGCAATTTGGGGAGTGAATATGGAAGCTTGCATAACACCTTACTCTGACCgtgagt-----acctttatctaatgtgctatataaaatgtttgatggcttttgcactttatttctatgctttgtctacaaattatagttatttctgttttactag

upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA10G32470.1 (Glycine max), 5'ss of exon 5
AGAGAACCTGGAACTCAGCCTCCTCTTTGCCGTTCTGATAATGACCCTGATGCTGTGTGGGGCGTAAACATGGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttcaagcttcttctcgcttttcaataacagcgtatatttcctctgaactct-----tttttggggttgtcttag-----------------------
||||||||||| ||||  |||||||||||||  |||||  ||||| | ||||| || ||||| ||||| ||| |||| ||||| ||  |||||||||| ||| |||  ||    ||||    | ||||   | |  |  | |   | |  || | |||     ||| |  |   || | |                        
AGAGAACCTGGTACTCGCCCTCCTCTTTGCCAGTCTGACGATGACTCAGATGCAGTATGGGGAGTAAATATGAAAGCATGCATAACACCTTACAGTGATCgtgagtactct--tttctcagtggttttt--ttatggtttttgcattccatggattctagcgatttctttgcgagtatcaattcattgttacttctttagtggc

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|124797499|gb|EH887178.1|EH887178
EST:     GGAAGCTTGCATTACTTCTTACAGTGACC                         T
genomic: GGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttc ... gttgtcttag-
EST: gi|124797499|gb|EH887178.1|EH887178
EST:     GGAAGCTTGCATTACTTCTTACAGTGACC                         T
genomic: GGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttc ... gttgtcttag-
EST: gi|47831830|gb|CK121514.1|CK121514
EST:     TGCTGTGTGGGGCGTAAACATGGAAGCTTGCATTACTTCTTACAGTGACC                         ATGACCACAAAACCAAGGGAAGTGGATTAGCTCCATGGCCAGCTCGGTTAA
genomic: TGCTGTGTGGGGCGTAAACATGGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttc ... gttgtcttagATGACCACAAAACCAAGGGAAGTGGATTAGCTCCATGGCCAGCTCGGTTAA
EST: gi|86079584|gb|DR375341.1|DR375341
EST:     GTAAACATGGAAGCTTGCATTACTTCTTACAGTGACC                         ATGACCACAAAACCAAGGGAAGTGGATTAGCTCCATGGCCAGCTCGGTTAA
genomic: GTAAACATGGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttc ... gttgtcttagATGACCACAAAACCAAGGGAAGTGGATTAGCTCCATGGCCAGCTCGGTTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAACCTGGAACTCAGCCTCCTCTTTGCCGTTCTGATAATGACCCTGATGCTGTGTGGGGCGTAAACATGGAAGCTTGCATTACTTCTTACAGTGACCgtaagttttcaagcttcttctcgcttttcaataacagcgtatatttcctctgaactcttttttggggttgtcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG