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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtatacagataaacagtttccgtactttgtgtgaatgattagttgtttactattgggattaatatttgcttggatcaacttag

Basic information

species Arabidopsis thaliana
transcript AT5G28840.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 5'ss of exon 4
GCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtatacagataaacagtttccgtactttgtgtgaatgattagttgtttactattgggattaatatttgcttggatcaacttag
|| || |||||| | || ||||| |||| ||| || ||||| |||||||| ||  ||||  | ||||| ||||| ||||| || |||||||||||||||||||| |     |  ||   |    ||  ||    || |    || | |   |   ||    | ||| | |   |||||        
GCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACAACATATATGGCCCCTTTGGAACATGGAAAGgtagaagtttaaccaattctccaagttattgaactgtacttgtactggggcatccttaac-tcaatttgtcaatggatag------

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA19G43400.1 (Glycine max), 5'ss of exon 4
GCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgta-gtatacagataaac----agtttccgtactttgtgtgaatga-ttagttgtttact--attgggattaatatttgcttggatcaacttag---------------------------
|| || || ||||| || |||||||| ||||| |||||||| |||||||| || ||||| || ||||||||||| |||||||||| ||| |||||||| |||| ||       | ||     |||||  | | ||  |||   ||| | | |    || |  |      ||  ||     ||||||  |   ||                           
GCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATAACATATATGGTCCTTATGGGACATGGAAGGgtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatag

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G40720.1 (Glycine max), 5'ss of exon 4
GCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgta-gtatacagataaac----agtttccgtactttgtgtgaatga-ttagttgtttactattgggatta----atatttgcttggatcaacttag---------------------------
|| || || ||||| || |||||||| ||||| |||||||| |||||||| || ||||| || ||||||||||| |||||||||| ||| |||||||| |||| ||       |  |     |||||  |   ||  |||   | | | ||| |  |  | | || |||      ||     ||||||  |   ||                           
GCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATAACATATATGGTCCTTATGGGACATGGAAGGgtatgttcttgactgcattgcaagtttttgcggttgttgtatttaagtcagtagact--tgtgggcattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatag

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G30400.1 (Glycine max), 5'ss of exon 3
GCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgta-gtatac----agataaacagtttccgtacttt--------------gtgtgaatgattagttgtttactattgggattaatatttgcttggatcaacttag-----------------------
|| || ||||| || || ||||| || ||||| |||||||| |||||||| || ||||| |||||||| ||||| || ||||||||||| ||||||||||| | || |        ||  | || ||   || |||              | || |||   ||||  |||  ||||  | | |   || |  |  |  || || |                       
GCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACAACATATACGGTCCTTTTGGGACATGGAAAGgcatgtttttcactgaattgaaagcttttatagttttgactttaccaaatgggtaaattggtagtcattttatattttggtaacctttcggatttaataagtttgtgttttgttgttttgtcatacag

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G36740.2 (Glycine max), 5'ss of exon 4
GCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtag----tatacaga--taaacagtttccgtactttgt---------gtgaatgattagttgtttactattgggattaatatttgcttggatcaacttag---------------------------
|| || ||||| || || ||||| || ||||| |||||||| |||||||| || ||||| |||||||| ||||| || ||||||||||| ||||||||||| |     || || ||  | || | |||      |||||          ||  | | | | |    | | |  |  ||  ||     ||||||  | | ||                           
GCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACAACATATACGGTCCTTTTGGGACATGGAAAGgcatgctttacactgaattgaaaacttttatagttttgtctttaccaaatgggtaaattggtagacattttatgttttggtaaccttttggatttaataagtttgtgttttgttgttttgtcatacag

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|116412576|gb|EG455168.1|EG455168
EST:     TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAG                         GTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
genomic: TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtataca ... atcaacttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
EST: gi|47830746|gb|CK120430.1|CK120430
EST:     TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAG                         GTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
genomic: TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtataca ... atcaacttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
EST: gi|124914015|gb|EH987889.1|EH987889
EST:     ACATTTATGGTCCTTTTGGAACATGGAAAG                         GTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAA
genomic: ACATTTATGGTCCTTTTGGAACATGGAAAGgtagtataca ... atcaacttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAA
EST: gi|86019686|gb|DR315432.1|DR315432
EST:     TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAG                         GTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
genomic: TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtataca ... atcaacttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
EST: gi|125116641|gb|EL166102.1|EL166102
EST:     CCATAACATTTATGGTCCTTTTGGAACATGGAAAG                         GTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
genomic: CCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtataca ... atcaacttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
EST: gi|116412564|gb|EG455156.1|EG455156
EST:     TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAG                         GTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
genomic: TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtataca ... atcaacttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
EST: gi|116460304|gb|EG502896.1|EG502896
EST:     TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAG                         GTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA
genomic: TCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtataca ... atcaacttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATAACATTTATGGTCCTTTTGGAACATGGAAAGgtagtatacagataaacagtttccgtactttgtgtgaatgattagttgtttactattgggattaatatttgcttggatcaacttag

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