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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCCACGATGGCTGAGCTTGCCAAACTCTTCCCTAATGAAATATCTGCAGACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattgaataaccagtctggcaatgtctttgttgttactgaactgatggtgacatttatagcccttacattcagctgtgttctgaatcctaatggaactactggctacattgtttcag

Basic information

species Glycine max
transcript GLYMA11G36810.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 5'ss of exon 13
AAGCCACGATGGCTGAGCTTGCCAAACTCTTCCCTAATGAAATATCTGCAGACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattgaataaccagtctggcaa-tgtctttgttgttactga----actgatggtgacatttatagcccttacattcagctgtgttctgaatcctaatggaactactggctacattgtttcag
|||| || |||   ||||| ||||| || || ||| |||||||  |||| || || || |||||||||||||| ||||| |||||||| || ||||||||||  |      |  | ||   | |   | |||    | | |  |      || || ||   ||  | |   ||  ||     || | || |   ||  | ||  ||                    
AAGCAACTATGCAAGAGCTAGCCAAGCTATTTCCTGATGAAATTGCTGCTGATCAGAGTAAAGCAAAGATTCTGAAGTATCATGTTGTGAAGACACCAAGgtgaggacattttgcaagagcgccccctatctgatatatcataggtaggtctaatagttggatgcacacttctctcacgttcctttcttttctgtctcactgttacag------------------

upper sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 12
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 5'ss of exon 13
AAGCCACGATGGCTGAGCTTGCCAAACTCTTCCCTAATGAAATATCTGCAGACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattgaataaccagtctggcaatgtctttgttgttactgaactgatggtgacatttatagcccttacattcagctgtgttctgaatcctaatggaactactggctacattgtttcag
| || || |||   || ||||  |||||||||||| ||||||| || || |||||||||||||| || ||||| ||||||||||| ||||| || ||||||||  | ||||        |     || |   |     |   | ||      | ||||| |||      ||||    || | || |    | | ||                         
ATGCAACAATGAAAGAACTTGAGAAACTCTTCCCTGATGAAATCTCAGCTGACCAAAGCAAAGCTAAAATTCTGAAGTACCATGTCGTTAAGACTCCAAGgtt--agtgaa--gttgtaccatttatttagcttcaaatgagggaccaggctttacattgataaattcaacatctttctctattgttg--catgatcag----------------------

upper sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 5'ss of exon 13
AAGCCACGATGGCTGAGCTTGCCAAACTCTTCCCTAATGAAATATCTGCAGACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattgaataa--ccagtctggcaatgtctttgttgttactgaactgatggtgacatttatagcccttacattcagctgtgttctgaatccta-atggaactactggctacattgtttcag
|||| || |||   || |||||||||||||| ||| ||||||| || | ||| || |||||||| ||  || | || |||||||||||||||||||||||||| || |||| ||   || |     |   |||||  | || ||    | ||    | ||     |||  | |||| |   ||      ||   || |  |||  |                  
AAGCTACAATGAAGGAACTTGCCAAACTCTTTCCTGATGAAATTTCAGAAGATCAGAGCAAAGCGAAAGTTTTGAAATACCATGTTGTTAAAACACCAAGgttagaatgaaaaaagtcatttatttatcatctttcct-tttcttttttaattaaaaaat-----gccaatccattgaatagtaaaaaaaaatgtacaaagaagga------------------

upper sequence: GLYMA11G36810.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S369_27V6.1 (Physcomitrella patens), 5'ss of exon 9
AAGCCACGATGGCTGAGCTTGCCAAACTCTTCCCTAATGAAATATCTGCAGACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattgaataaccagtctggcaatgtctttgttgt----tactgaactgatggtgacatt--tatagcccttacattcagctgtgttctgaatcctaatggaactactggctacattgtttcag-----------------
| || || ||||  ||||| |||||| | ||||| ||||||||  | || |||||||| ||||| ||||||||||||||||| || || ||||| |||||||   |   | |   ||  ||      | ||    ||     | || || |  |  | |  ||    |     | |  ||  ||      | | |   | ||| |   ||  |  |     |||| |                 
ATGCAACAATGGAAGAGCTAGCCAAATTGTTCCCCAATGAAATTGCAGCTGACCAAAGTAAAGCCAAGATTCTCAAGTACCACGTGGTGAAAACTCCAAGgtactaagaactttacaccctactgtgggctcatctgcactatgctaaatttcttttaattttgccgtgtgtttgatttttcgcaagcaccagtagttttatgaattcacgagtaagcccttttctgaccgctgcatctttcag

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|120494098|gb|EH222265.1|EH222265
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
EST: gi|120494096|gb|EH222263.1|EH222263
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
EST: gi|51336354|gb|CO980220.1|CO980220
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
EST: gi|151398360|gb|EV268231.1|EV268231
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTATAAAG
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
EST: gi|9259861|gb|BE348008.1|BE348008
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
EST: gi|12773974|gb|BG238901.1|BG238901
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTTCAAATTGTGAAACCTTGTCGTCCCCTTACAA
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAA-CCTTGTCGTCCC-TTACAA
EST: gi|209709797|gb|BW657248.1|BW657248
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
EST: gi|209729339|gb|BW663640.1|BW663640
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
EST: gi|13787271|gb|BG649863.1|BG649863
EST:     GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAG                         GTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG
genomic: GACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattga ... attgtttcagGTCAGTTTACAAAACTGTTCCAAATTGTGAACCTTGTCGTCCCTTACAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCCACGATGGCTGAGCTTGCCAAACTCTTCCCTAATGAAATATCTGCAGACCAAAGCAAAGCAAAGATTCTCAAGTACCATGTTGTTAAAACACCAAGgtttgattgaataaccagtctggcaatgtctttgttgttactgaactgatggtgacatttatagcccttacattcagctgtgttctgaatcctaatggaactactggctacattgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG