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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgggcttaatttcatcttcttttttttttctctctttcttttttatcctttgtttctctcttaatataagttcaatctatgtttctctcttaagatattcatgtgttgttgctttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGCTGCCGCCACCGCTGCAGCTGGTGGTGTATCCGGATTTGAGTTTGGCGTG

Basic information

species Glycine max
transcript GLYMA11G08290.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 5
gtttgtgggcttaatttcatcttcttttttttttctctctttcttttttatcctttgtttctctcttaatataagttcaatctatgtttctctctta-agatattcatgtgttgttgctttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGCTGCCGCCACCGCTGCAGCTGGTGGTGTATCCGGATTTGAGTTTGGCGTG
                  | ||  |    |||   | | ||| ||||| || ||    |    |  ||  | |   | |   | |  ||   ||||| | ||  |  ||| ||||| | |  ||||||||| || || || || || |||||||||||||||||||||||||| || ||||||||| | || ||||||||||||||  | || ||||| ||||| |||
----------------gtaactggtcaactttcattttttttttttttcattctcgcatgacattgtagaaaattatgacagtgtaatttcatcttatatattcttttgttttgtttcctcatggcagTACACCCATCTTCACAGGGGATGGGGAAGGTGGAAGTGGTTTTGCAGCAGCTGCCGCCGCAGCAGCAGCTGGTGGTGTGGCTGGTTTTGATTTTGGTGTG

upper sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S14_318V6.2 (Physcomitrella patens), 3'ss of exon 5
gtttgtgggcttaatttcatcttcttttttttttctctctttcttttttatcctttgtttctctcttaatataagttcaatctatgtttctctcttaagatattcatgtgttgttgctttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGCTGCCGCCACCGCTGCAGCTGGTGGTGTATCCGGATTTGAGTTTGGCGTG
                           |  | ||   |     | |  |    | |  |   |||||  || | | |   | |  || || |   |       | || | | ||| ||    | |||| |  |||| |||||||||||||| |||||||||||||| |||||||| ||||| ||| |  |||| || |  | ||     ||   ||    ||| |  
--------------------------atgatcttactttgaattctgatggtttgtactggcctcttggtaaatgatatgttttggtatcaccagtctctctctaatttatggttactccacg-cagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA
















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|151409810|gb|EV279618.1|EV279618
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
EST: gi|193437556|gb|FK399125.1|FK399125
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACT
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACT
EST: gi|208307246|gb|GE108772.1|GE108772
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTCTTGCTGCTGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
EST: gi|193726802|gb|FK661556.1|FK661556
EST:     GCTCTTTCTGATGTACTTATAAG                         TACGCCTA-TTTTACTGGTGAT-GGGAAGGTGGAAGTGGTTTTGCTGCTGC
genomic: GCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
EST: gi|254318747|gb|GR830311.1|GR830311
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
EST: gi|193565473|gb|FK527252.1|FK527252
EST:     GCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGAT-GGGAAGGGTGGAAGTGGTTTTGCTGCTG
genomic: GCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAA-GGTGGAAGTGGTTTTGCTGCTG
EST: gi|193385969|gb|FK352367.1|FK352367
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
EST: gi|193366825|gb|FK331511.1|FK331511
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACT
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACT
EST: gi|208055326|gb|GD854981.1|GD854981
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
EST: gi|193437518|gb|FK401803.1|FK401803
EST:     GTTCATGTTCCATCTGGTCCAAATGTCTTCTTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACT
genomic: GTTCATGTTCCATCTGGTCCAAATG-CT-CTTT-CTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACT
EST: gi|193551284|gb|FK508013.1|FK508013
EST:     TCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGATGGGGAAGGGTGGAAGTGGTTTTGCTGCTG
genomic: TCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAA-GGTGGAAGTGGTTTTGCTGCTG
EST: gi|151395379|gb|EV265250.1|EV265250
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
EST: gi|193562994|gb|FK520813.1|FK520813
EST:     GATGTACTTATAAG                         TACGCCTATTTTTACTTGGTGATGGGGAAGGGTGGGAAGTGGTTTTGCTGC
genomic: GATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTAC-TGGTGATGGGGAA-GGT-GGAAGTGGTTTTGCTGC
EST: gi|193366550|gb|FK332916.1|FK332916
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACT
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACT
EST: gi|151397896|gb|EV267769.1|EV267769
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGC
EST: gi|193425763|gb|FK391730.1|FK391730
EST:     ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAG                         TACGCCTATTTT
genomic: ATTGTTCATGTTCCATCTGGTCCAAATGCTCTTTCTGATGTACTTATAAGgtttgtgggc ... tttgtggcagTACGCCTATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttcaatctatgtttctctcttaagatattcatgtgttgttgctttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGCTGCCGCCACCGCTGCAGCTGGTGGTGTATCCGGATTTGAGTTTGGCGTG
                                         ttgcttt  CT-rich tract
                      ttaagatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgggcttaatttcatcttcttttttttttctctctttcttttttatcctttgtttctctcttaatataagttcaatctatgtttctctcttaagatattcatgtgttgttgctttgtggcagTACGCCTATTTTTACTGGTGATGGGGAAGGTGGAAGTGGTTTTGCTGCTGCTGCCGCCACCGCTGCAGCTGGTGGTGTATCCGGATTTGAGTTTGGCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG