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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaattgttacaaaacatctgtgtacttgtcttgttagagtagttttattcatagaagattgtgttttttttttgtccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCTCTTTGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCC

Basic information

species Arabidopsis thaliana
transcript AT5G27470.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G37700.1 (Glycine max), 3'ss of exon 5
---gtatttaattgttac-aaaacatctgtgtact--tgtcttgttagagtagttttattcatagaagattgtgtttttttt---------ttgt-ccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCTCTTTGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCC
    | | |||||||||  |  | |  |   || |  |        | |  | |   |     |  |  || || ||| | |         || | | |||| ||||||||||||||||||||||| || |||||||| ||||||||||| || ||||| || ||| | ||||| ||||| || || ||  |||| ||  
tgtttttgtaattgttattatgataggtaaataataatagacgacaaaaccaataccaccttaaccattttctggtttatctaagaagttattatgctagGTAACTGGTGAAGGAGATGACAAATATCTGATTGCAACAGCTGAGCAGCCACTCTGTGCATATCATTTAGATGATTGGATCCACCCTACCCAGCTACCAT

upper sequence: AT5G27470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G29600.1 (Glycine max), 3'ss of exon 5
--------------------gtatttaattgttacaaaacatctgtgtacttgtcttgttagagtagttttattcatagaagattgtgttttttttttgtccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCTCTTTGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCC
                     |   ||| |  ||  | | | |     |  | ||   ||| | || |||| |   |  |    |  |  ||| || |||  |||| ||||||||||||||||||||||| || |||||||| || |||||||| || ||||| || ||| | ||||| ||||| || || ||  |||| ||  
cttttgtatttgttattatgctgggtaaataataacagataacaaaacaaatatcacctta-actatttttttgagtttat--ctaagaatttattatgtt-agGTAACTGGTGAAGGAGATGACAAATATCTGATTGCAACAGCAGAGCAGCCACTCTGTGCATATCATTTAGATGATTGGATCCACCCTACCCAGCTACCAA

upper sequence: AT5G27470.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S142_120V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------gtatttaa--ttgttacaaaacatctgtgtact--tgtcttgttagagtagtttta--ttcatagaagattg-------tgttttttttttgtc-cagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCTCTTTGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCC
                                               | | |||  |||||  || ||    | | |    ||| ||   |||| |  || |  ||| | ||  ||||       ||    |  | ||   ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||| ||| | || || |  |||  ||     |||||  | || |   |  | ||| 
gttagcaccatctttatcttccattcgcattcctttgagtatgataatttctaagtttgttgaaagacgagagaggatcaatgtattagaagagcatattcagcttcgtggattattgattcgcatgacactggtctgctacagGTGACTGGGGAAGGTGATGATAAATACCTCATCGCTACTGCCGAGCAACCTTTGTGCGCATTGCATCGTGGCAGTTGGATGGACCCAAAGCAATTACCCA

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|125283396|gb|EL297481.1|EL297481
EST:     GTTCGATGAAGAGCTTTACAAG                         GTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCT
genomic: GTTCGATGAAGAGCTTTACAAGgtatttaatt ... ttttgtccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCT
EST: gi|164046166|gb|ES167121.1|ES167121
EST:     GGCCAAGTGCGCACAATTGGCACAGTTCGATGAAGAGCTTTACAAG                         GTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGC
genomic: GGCCAAGTGCGCACAATTGGCACAGTTCGATGAAGAGCTTTACAAGgtatttaatt ... ttttgtccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGC
EST: gi|86059858|gb|DR355615.1|DR355615
EST:     TATGGCCAAGTGCGCACAATTGGCAAAAGTTCGATGAAGAGCTTTACAAG                         GTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCT
genomic: TATGGCCAAGTGCGCACAATTGGC-ACAGTTCGATGAAGAGCTTTACAAGgtatttaatt ... ttttgtccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCT
EST: gi|47831831|gb|CK121515.1|CK121515
EST:     TTATGGCCAAGTGCGCACAATTGGCACAGTTCGATGAAGAGCTTTACAAG                         GTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCT
genomic: TTATGGCCAAGTGCGCACAATTGGCACAGTTCGATGAAGAGCTTTACAAGgtatttaatt ... ttttgtccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcttgttagagtagttttattcatagaagattgtgttttttttttgtccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCTCTTTGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCC
                                     tgttttttttttgtcc  CT-rich tract
                                 attgtgtttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttaattgttacaaaacatctgtgtacttgtcttgttagagtagttttattcatagaagattgtgttttttttttgtccagGTGACTGGTGAAGGAGATGACAAATACCTCATTGCAACTGCTGAGCAGCCTCTTTGTGCGTACCATATTGATGAATGGATTCATCCGACTGAGCTTCCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT