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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcatgtgtcattgtcctttatactcttagatgtgagttctgatcgctgaacaccatgctctatcaataaataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGAAAGGAGGCTCGTCGATCAAATGCTATCTTACACAAG

Basic information

species Arabidopsis thaliana
transcript AT3G55610.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 7
---------------gtatgtcatgtgtcatt--gtcctttatac-tcttagatgtgagttctgatcgctgaacaccatgctctatcaataaataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGAAAGGAGGCTCGTCGATCAAATGCTATCTTACACAAG
                |  | |    |   ||   |   ||||   | ||| |||    || | | |  |  |     |    | | |  |  | || |||||||||||||| |||||||| ||||| ||||| |||||  |||| ||||| || || |||   || |||||||| || || ||||| 
gtatgaatgaaccttatgagcctaaagctgtttgattgattatctgtattatatgctgtttatcaacattttaagtggtagcttcttatcatctgaa-cagATAGCTTCGCTGGCAATCCGAAGTGGGAATGGGCTTCTCTTGAAAGGTGGCAAAGAAGCTAAGCGGTCAAATGCAATTTTGCACAAA
















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|124717733|gb|EH809135.1|EH809135
EST:     TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAG                         ATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTC
genomic: TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAGgtatgtcatg ... aataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTC
EST: gi|86042495|gb|DR338250.1|DR338250
EST:     TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAG                         ATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGA
genomic: TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAGgtatgtcatg ... aataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGA
EST: gi|86042492|gb|DR338247.1|DR338247
EST:     TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAG                         ATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGA
genomic: TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAGgtatgtcatg ... aataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGA
EST: gi|86042493|gb|DR338248.1|DR338248
EST:     TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAG                         ATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGA
genomic: TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAGgtatgtcatg ... aataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGA
EST: gi|86042496|gb|DR338251.1|DR338251
EST:     TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAG                         ATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGA
genomic: TAGGTGTTCTTCTGATTGTTTTTGAATCCCGGCCTGATGCACTTGTTCAGgtatgtcatg ... aataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttagatgtgagttctgatcgctgaacaccatgctctatcaataaataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGAAAGGAGGCTCGTCGATCAAATGCTATCTTACACAAG
             ttctgat  putative branch site (score: 3)
                                   tctatcaataaataaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcatgtgtcattgtcctttatactcttagatgtgagttctgatcgctgaacaccatgctctatcaataaataaaacagATAGCTTCGCTTGCAATCCGGAGTGGAAATGGTCTTCTGCTGAAGGGTGGAAAGGAGGCTCGTCGATCAAATGCTATCTTACACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG