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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgttattcatggttacttctgtgagcttccaccttcttgtttattgcacctgctttattcttttcttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT

Basic information

species Arabidopsis thaliana
transcript AT1G31810.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA09G34830.1 (Glycine max), 3'ss of exon 14
----------------gtatgcttgttattcatggttac---ttctgtgagcttccaccttcttgtttattgcacctgctttat-tcttttcttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT
                 | |  |  || || ||  | |    ||      | ||  |  |     |   ||||   || ||  | |  | | |  || ||  ||||| || | ||| | |||||||||||||||||||| | || ||||||  | || || |||||||||||||||   ||||| |||||||||||||| || |
gtattctctgtcactaatgttttcattgttgatattgatgtattacagatgattttatgtaagattactttgcttatgattggtattctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTCGCTGCTTCTGAAAATGATGGTGCTATAT

upper sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 14
---------------gtatgcttgttattcat---ggttacttctgtgagcttccaccttcttgtttattgcacctgctttattcttttc--ttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT
                  |  |  ||||| ||   | |   ||    | | ||  |  |     | | ||||   ||  ||  | || ||  |  || ||  ||||| || | ||| | |||||||||||||||||||| | || ||||||  | || || ||||||||||||||    ||||| |||||||||||||| || |
gtattctttgtcgctaatttttcattattgatatagatgtattacaggtgattttatgtaagattattttgcttatgtattgatgttctctgtccaatatctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTTGCTGCTTCTGAAAATGATGGTGCTATAT

upper sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 14
------------------------------------------gtatgcttgtt--attcatggttacttctgtgagctt--ccaccttcttgtttattgcacctgctttattctt--ttcttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT
                                           |  | |||||  | |  |    || |     |||||  |    |  ||  || |||   ||  |  ||| |   |||  |   |   ||||| |||||||| | ||||| || ||||||||||| | || |||||| |||||||||||||||||||||||||  || || |  ||||||||||| || |
gtatgcttaacatgtcaaaagtattgtccccgcagctctttgcttagtttgtttaacttgtaacaacattccatagcttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT

upper sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S246_71V6.1 (Physcomitrella patens), 3'ss of exon 14
-----------gtatgcttgttatt-catg-gttacttctgtgagcttccac-cttcttgtttattgc--acctgctttattcttttcttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT
           |  | ||||| ||   ||  | |||     |||    |||  |||| | |   ||||  |||  | |     || |  |     || ||||| |||||||  |||||||||||||||||||||| |  |  || || ||||| || || || |||||| |       ||||||||||| ||| |    |
agtgtctagttgcttacttgtgatagtatatgatacaatattgattggccaagcttcgtttaccttgctaaccaacatatcatttgttgtgcgtctgtagATTCAATTGAAGTCGTTGGCTGAAGAAATGCAAGCAGTTAGCAAGGGTCTTGAGAAAGTCGAACAAGAAATTGCTATGTCAGAAAATGACGGTCCTCCAT

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|86044354|gb|DR340109.1|DR340109
EST:     AATTGCTGGATTTTGCTAATGACCTTGTTCACTTAGAAGCTGCTTCAAA-                         ATTGAATTTGAAA-CGTTGGCTGAA
genomic: AATTGCTGGATTTTGCTAATGACCTTGTTCACTTAGAAGCTGCTTCAAAGgtatgcttgt ... aaaaatgcagATTGAATT-GAAAACGTTGGCTGAA
EST: gi|86044355|gb|DR340110.1|DR340110
EST:     AATTGCTGGATTTTGCTAATGACCTTGTTCACTTAGAAGCTGCTTCAAAG                         ATTGAATTGAAAACGTTGGCTGAAGAAGTGCAAGCGGCGACTAAAGGCCTT
genomic: AATTGCTGGATTTTGCTAATGACCTTGTTCACTTAGAAGCTGCTTCAAAGgtatgcttgt ... aaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcttccaccttcttgtttattgcacctgctttattcttttcttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT
                              ctttattcttttctta  CT-rich tract
                               tttattcttttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttgttattcatggttacttctgtgagcttccaccttcttgtttattgcacctgctttattcttttcttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC