Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgaggcacggaatggaactaacgttgcttattggatttgcggtttctgtaaccttcaaatggtttgaaaatgcag

Basic information

species Arabidopsis thaliana
transcript AT4G37930.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 5'ss of exon 10
GTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgagg-cacggaatggaactaacgttgcttattggatttgcggtttctgtaacc--ttcaaatggtttgaaaatgcag-------------------
 || || | ||||||||| || ||    ||||| || || || || ||||| ||||| ||||||||||| ||  ||||||| |||||||| ||||||||||||   |   | || |  ||  |  |||||  |   ||    |   || | |  | ||    || ||  |  |  ||||||||                    
CTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAAACAGgtaaactttcgtcatgcgatc-atttaacgaggagcat-aactcatcgatattggaaagaggtttaagcgaatc-aaaatgcaaaacttcaccttttttaatg
















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|124936363|gb|EL013273.1|EL013273
EST:     CACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: CACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|124990134|gb|EL062403.1|EL062403
EST:     ACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: ACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|124820296|gb|EH905162.1|EH905162
EST:     AGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: AGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|152034927|gb|BP840236.2|BP840236
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|124839727|gb|EH924166.1|EH924166
EST:     TGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAAACAG                         GCAACTACTTCAGAGTACAAAGCA
genomic: TGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAA-CAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCA
EST: gi|125217003|gb|EL231086.1|EL231086
EST:     GTGGTCCACACAACCACACTATCGCAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|125211151|gb|EL226105.1|EL226105
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATAC
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATAC
EST: gi|116443767|gb|EG486359.1|EG486359
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|116484717|gb|EG527309.1|EG527309
EST:     CCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAGCAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: CCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|125108440|gb|EL161352.1|EL161352
EST:     CAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: CAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|86079465|gb|DR375222.1|DR375222
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|116484716|gb|EG527308.1|EG527308
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAGCAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|125261145|gb|EL275230.1|EL275230
EST:     CAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAGCAAGTCCTGAGTAACAGT
genomic: CAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|124754673|gb|EH844803.1|EH844803
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGT
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGT
EST: gi|124724542|gb|EH815944.1|EH815944
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAA
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAA
EST: gi|125032647|gb|EL104916.1|EL104916
EST:     CACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: CACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|125029928|gb|EL102197.1|EL102197
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAG
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAG
EST: gi|125278212|gb|EL292297.1|EL292297
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCAT
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCAT
EST: gi|125132248|gb|EL174426.1|EL174426
EST:     TGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGA
genomic: TGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGA
EST: gi|125023647|gb|EL095916.1|EL095916
EST:     ACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: ACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|116484725|gb|EG527317.1|EG527317
EST:     GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
genomic: GTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACAGT
EST: gi|125025398|gb|EL097667.1|EL097667
EST:     TGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAG                         GCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGGGTAACA
genomic: TGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgag ... gaaaatgcagGCAACTACTTCAGAGTACAAAGCATACCAAGAACAAGTCCTGAGTAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGAAACAGgtacggtgaggcacggaatggaactaacgttgcttattggatttgcggtttctgtaaccttcaaatggtttgaaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT