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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat...

Basic information

species Glycine max
transcript GLYMA13G42360.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat
 |||||||||||  | ||||| ||||| || || ||   ||| |||||||||||  | ||||| |||||||||||||| || |||||||||||||| |||||||| |   | | | |    |||| ||   |  |     | |  ||   ||||||       ||   |      ||| | |  || || || |      
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgtta--tcttcttcaaagtttgaa---tctaccctctgtggttatctctgatattgacttggttttgtgttgttttctggtgaat-ttgcag----

upper sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat
 ||||||||| |   ||| |||||||||||| | ||  |||| |||||||||||| | ||||| |||||||||||||| || |||||||||||||||||||| ||    | || |    | |||| ||        | ||| |  |||    ||| || | ||||   |||    ||| |||||                
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagt-gtttcaattccattctcgttatagtttaacttgaatc-tcactggtttctgg--gttttttcag---------------

upper sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat
 |||||| || |||| ||||| || || ||| | |||   || || ||||||||| | ||||| |||||||||||||| ||||||||||||||||| ||||||| ||  | ||  || |    ||   |||||   || ||||| | |||  | |   |      |  | |     |  ||| ||   |  |  ||    
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattc--acatt---ttctttttctctctgataaaatcaagtcatt-tgttcttataatttgatttct-ctgtcag---

upper sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv09s0002g01760.t01 (Vitis vinifera), 5'ss of exon 4
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttt---tccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcat----ctaaacgttct---ttcatgcatgttaccaatat--------------------------------------------------------------------------------
 ||||||||| | ||||||||||| ||||| |||||| |||| ||||||||||| |||||||||||||||||||||||||| || ||||||||||| ||||| || |   ||   ||  ||||| ||||  |  |  |||  ||||   | ||||    |   ||   | ||    ||||  |||     |||||||   || |  ||                                                                                  
GTTTGACATGTTGCGGAGACAGTCACTTCGCCCAGATTACATTAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtctgttctattatatctctgtttctttactagttgtaatatttttgcatacttcatggtgaagaacattattttgctaattgttagaagttcatgctcattgcttattgctggatttttcaatatgtgcaagttttgactggctttgttgtttttctgataattcattaattttttttgctgctgtcag

upper sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 4
lower sequence: PP1S77_16V6.1 (Physcomitrella patens), 5'ss of exon 3
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgttttttttt-cttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat------
 |  |||||| | || ||  |  | || ||  | |||  ||| |||   || ||  |||| ||||| ||||| ||||||||||| |||||||||||||||||  | ||  ||    |  ||| |       |||  |||||      | |   |||    |    |  |  |    |||   || ||  ||  | |  | |      
GTACGACATGTTGCGCAGGAATGCGCTGCGCGCGGATTCCATCAAGTGCTTCGTGCTGGACGAGGCCGATGAGATGCTTTCTCGGGGTTTCAAGGACCAGgtgcggtg--ttgttgtcgttgctgttgttgttg--ttgttgccaggtgccggtgagcgtttgtggagaatt--gtgtttggtcgtg-gtgggagcggtgtggatgg

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|192327065|gb|FK019282.1|FK019282
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAG                         ATCTCTGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggt ... tgaaatgcagATCTATGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGTTC
EST: gi|15813655|gb|BI785930.1|BI785930
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAG                         ATCTATGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggt ... tgaaatgcagATCTATGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGTTC
EST: gi|192306617|gb|FG998813.1|FG998813
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAG                         ATCTATGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGTTC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggt ... tgaaatgcagATCTATGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGTTC
EST: gi|254347906|gb|GR854155.1|GR854155
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAG                         ATCTATGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGT-C
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggt ... tgaaatgcagATCTATGACATCTTCCAGCTTCTGCCGGGTCAAATTCAGGTTGGAGTGTTC
EST: gi|209726515|gb|BW658082.1|BW658082
EST:     TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAG                         ATCTATGACATC
genomic: TTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggt ... tgaaatgcagATCTATGACATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT