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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctttttactacttctgcatgatgtttgtggtcacttagcctctgacatttggattgttcactgtattatttgtcaacatcaaaatggtgtc...

Basic information

species Glycine max
transcript GLYMA05G37850.3
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctttttactacttctgcatgatgtttgtggtcacttagcctctgacatttggattgttcactgtattatttgtcaacatcaaaatggtgtc----------------------------------------------------------------------------------
|||||||||||| | ||| | |||||||||||||||||||| || || ||||| |||||||||||||| ||||||||||||||  ||   |||  |    | | ||||     |||||  |    ||  || ||   | |||  |         | ||   || ||||  || |   ||                                                                                    
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagcttact----cctttgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtca-agtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag

upper sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 12
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtgg-------cctttttactacttctgcatg---atgtttgtggtcacttagcctctgacatttgg-attgttcactgtattatttgtcaacatcaaaatggtgtc-------------------------------------------------------------------
|| ||||||||| | ||| | |||||||||||||||||||| || || ||||| |||||||||||||| |||| |||||||||  ||         |||||  ||| ||| || ||     |     | |     | | |  ||   |   | |    | |  | |     | |  ||||    |  ||                                                                      
GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGGgtttgttagcttactcctttgcacttcttttgtatttctgtacagtttgcagtgtggtcattggtgtcaagtagaagtaaacgcaaggagtttggacatgggtactgtagtaatgtatatcttccatgttctataggaagaattttgaaccagttttggaattggtatttgtatacag

upper sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G111579_T01 (Zea mays), 5'ss of exon 11
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctttttact----acttctgcatg-atgtttgtg-gtcacttagcctctgacatttgg--attgttcactgtattatttgtcaacatcaaaatggtgtc-----------------------------------------------------
|| ||||| ||||||||  | |||||||||||||||||||| || || ||||| ||||||||||| || || |||||||||||  |||  ||  || |     |||||    || ||   ||||     ||  ||||||||||    |   ||  |     |||    | || ||   |  |   | |                                                      
GTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGGgtttgtgatctgctttcctttgacttcgttttgtattcctgtgcactgctgtgcctctgacagccagtagttaatatgaatatgggctatctacggtattagtttatttatagcttttgctagaagttttaaccagaatttggcttcatgcgagtccacag

upper sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc---tttttactacttctgcatgatgtttgtggtcacttagcctctgacattt--ggattgttcactgtattatttgtcaacatcaaaatggtgtc------------------------------------------------
|| ||| | ||||| ||  | |||||||||||||||||||| || || ||||| |||||||||||  | || |||||||||||  |||  |   |||    |   | ||  |  | ||| ||  ||||  ||| ||||||        ||  |  |  |||  | | ||  |   |  |   | |                                                 
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcact--gccactgacagccacaagttaatatcaatatggtctctctgcggtagtagtttatttctagtttttgctggaagttttaatcagaattttgtttatgtctacag

upper sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 12
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctttttactacttctgcatgatgtttgtggtcacttagcctctgacatt-tggattgttcact--gtattatttgtcaacatcaaaatggtgtc
||  || ||||||| || |||||||||||||||||||||||||| || ||||| ||  |||||||  | ||||| || ||||| | |     | |||  || | |  ||   ||   |  | |    |  ||  | | | | || ||||   |   | |||| |   ||  |||          
GTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGGgtaactacatctattagcacatatatatttcgtgcttaatgagaatgtttcaaaaagtattgactgttgttttgattttatctacaaatttcag---------

upper sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctttttactacttctgcatgatgtttgtggtcacttagcctctgacatttggattgttcactgtattatttgtcaacatcaaaatggtgtc----
|||||||||||||| || ||||| ||||| ||||||||||||||||| ||||| || || |||||||| ||||||||||||||   | |||| || |  |  | |  ||    |     | || || |    |||  |  | | |  ||| |   | || |||    |  ||     | |     
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcctcttca--atctgtatatttattacaaagccagtttgtacatgat-tcagtaatcatcagtac-tcatctgtatggaataagtgtatcttttcc

upper sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 5'ss of exon 11
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctt--tttactacttctgca-tgatgtttgtggtca--cttagc---ctctgac-atttggat-tgttcactgtattatttgtcaacatcaaaatggtgtc----------------------------------------------
|| ||||| ||  | |||||||||||||| || |||||||| || || ||| || |||||||||| || || |||||||||||  || | |     | | || |  |  |  ||     ||||  |  || |||    || ||| |  || || |  |     ||             ||| |   |||                                                
GTGAGGCTAAAACGTTATTTGGAGATGAGGGGAGCTGATGGTGGTCCATGGCGACGATTGTGTGCATTGCCTGCATTTTGGgtacgttgacgaagctcattattcttataacgaaaacggtggatagactgagcaacttccgaccaactgaatatacttgtcataacgagcagtgtactcagacgagtggtagcaagcctgctttgtttactcaagaaatgcgtttgttgtttgtag

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|209718855|gb|BW669042.1|BW669042
EST:     GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|12691343|gb|BG157679.1|BG157679
EST:     GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|13480024|gb|BG509367.1|BG509367
EST:     GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|9900602|gb|BE609570.1|BE609570
EST:     TGCTGATGGAGGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: TGCTGATGGA-GGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|192303006|gb|FG997022.1|FG997022
EST:     TTGGAGAAGATTGTGTGCTTTACCAGCATTTT--                         G--GGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: TTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|213588137|gb|DB979215.1|DB979215
EST:     GTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: GTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|120494105|gb|EH222272.1|EH222272
EST:     GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|19453403|gb|BM954813.1|BM954813
EST:     GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|192299708|gb|FG990032.1|FG990032
EST:     GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACG
genomic: GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|192303005|gb|FG997021.1|FG997021
EST:     GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTT--                         G--GGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
EST: gi|209707542|gb|BW665001.1|BW665001
EST:     GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG                         GTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA
genomic: GTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc ... attgtgtcagGTAGGGTTATTGTACGATGAACTTTCTCTAAAAAGTGTTTTGGATATGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcctttttactacttctgcatgatgtttgtggtcacttagcctctgacatttggattgttcactgtattatttgtcaacatcaaaatggtgtc

- - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA