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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttctttctttaaacctaatgagaaaatatttggttttctatttaagttttccatttagaaattttttggttcattttcacatgtctaaatatatgcattgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCAATCCATCAGACCCCTTAAATGGTGAAGCTGCAGCTTTAATGATGCGGGA

Basic information

species Glycine max
transcript GLYMA07G07540.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G07540.3 (Glycine max), 3'ss of exon 3
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 4
gtaatgttctttctttaaacctaatgagaaaatatttgg---ttttctatttaagttttccatttagaaattttttggttcattttcacatg------tctaaatatatgcat----tgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCAATCCATCAGACCCCTTAAATGGTGAAGCTGCAGCTTTAATGATGCGGGA
||||  ||  |  ||  | |  | |   |  || |  |    || ||| | ||   ||  |  |   |  |||| |  |   || | ||| |      | | ||  ||||  |    | || ||||||||||||||||||| ||||| || || |||||||||||  | ||||| ||||| || || || |||||||| || || || || || |||||||| ||
gtaagattgatctttacatctcattattaggatctccgcgccttatctgtatacaattagcgctcc-atgttttgtactctgttataacagggttaactttgaacctatgtgtgatattttgcagATCTTGTCAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA
















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|6914865|gb|AW396395.1|AW396395
EST:     GTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTG                         ATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
genomic: GTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTGgtaatgttct ... attgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
EST: gi|58023135|gb|CX709876.1|CX709876
EST:     AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTG                         ATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
genomic: AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTGgtaatgttct ... attgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
EST: gi|31464781|gb|CD406794.1|CD406794
EST:     AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTG                         ATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
genomic: AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTGgtaatgttct ... attgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
EST: gi|10252837|gb|BE820603.1|BE820603
EST:     AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTG                         ATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
genomic: AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTGgtaatgttct ... attgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
EST: gi|14011775|gb|BG726697.1|BG726697
EST:     AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTG                         ATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
genomic: AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTGgtaatgttct ... attgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
EST: gi|15812810|gb|BI785085.1|BI785085
EST:     AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTG                         ATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
genomic: AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTGgtaatgttct ... attgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
EST: gi|23730924|gb|BU763571.1|BU763571
EST:     AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTG                         ATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
genomic: AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTGgtaatgttct ... attgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
EST: gi|151400703|gb|EV270517.1|EV270517
EST:     AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTG                         AACTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA
genomic: AGGATCAGTTTGTCTTGATGTTATCAATCAAACCTGGAGTCCCATGTTTGgtaatgttct ... attgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttagaaattttttggttcattttcacatgtctaaatatatgcattgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCAATCCATCAGACCCCTTAAATGGTGAAGCTGCAGCTTTAATGATGCGGGA
                               gtctaaa  putative branch site (score: 3)
                                              ttgtttc  putative PPT
                             atgtctaaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttctttctttaaacctaatgagaaaatatttggttttctatttaagttttccatttagaaattttttggttcattttcacatgtctaaatatatgcattgtttcagATCTTGTCAATGTGTTTGAGGTGTTTCTACCACAACTTCTTCTGTATCCCAATCCATCAGACCCCTTAAATGGTGAAGCTGCAGCTTTAATGATGCGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT