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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATTTGAAAAGTCACTGCAGTATGTGAAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGAgtatccttctaaactaaattgaataacccatttgtcatttcagttaaattatgttgaatgtttatgtcagtgtcctgttcttttagaaaatttggcccaa...

Basic information

species Glycine max
transcript GLYMA16G09890.1
intron # 3
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G09890.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTATTTGAAAAGTCACTGCAGTATGTGAAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGAgtatcctt---ctaaactaaattgaataacccattt---gtcatttcagttaaattatgttgaatgtttatgtcagtgtcctgttcttttagaaaatttggcccaa-------------------------------------------
 || ||||| |||||  |||| |||||||| || ||||| ||||| || ||||| |||||||| ||||||||||||||||||||||   || || ||  |||| | |    |||   || ||    | |     ||| |   |  ||   | ||||   | ||    |      |||    | |                                           
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttttctgaattagtttgattcaaagtttttaagtaatcgttgctttgacatgcttccttcttg-atgagtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag
















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|192329760|gb|FK022984.1|FK022984
EST:     AAACGCTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGAgtatccttct ... tgccatacagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|208326961|gb|GE123709.1|GE123709
EST:     CTGTCAGACTAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: CTGTCAGAC-AAGTTCGAGAgtatccttct ... tgccatacagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|207762346|gb|GD732059.1|GD732059
EST:     GTCAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: GTCAGACAAGTTCGAGAgtatccttct ... tgccatacagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|208191571|gb|GD991015.1|GD991015
EST:     CTGTCAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: CTGTCAGACAAGTTCGAGAgtatccttct ... tgccatacagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|7145703|gb|AW507625.1|AW507625
EST:     AAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGA                         GATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGAgtatccttct ... tgccatacagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|10254879|gb|BE822645.1|BE822645
EST:     AAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGAgtatccttct ... tgccatacagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|192303824|gb|FG998176.1|FG998176
EST:     AAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGAgtatccttct ... tgccatacagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATTTGAAAAGTCACTGCAGTATGTGAAACGTTTCAGTCGCTATAAAAATCCTGATGCTGTCAGACAAGTTCGAGAgtatccttctaaactaaattgaataacccatttgtcatttcagttaaattatgttgaatgtttatgtcagtgtcctgttcttttagaaaatttggcccaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG