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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcctaaactaaattgaataacccgtttgtcatttctctttgtccatacatttactttcggttaaataatgttgaattttgatgtaaatgtcctg...

Basic information

species Glycine max
transcript GLYMA05G32260.1
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: GLYMA05G32260.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctc---ctaaactaaattgaataacccgtttgtcatttctctttgtccatacatttactttcggttaaataatgttgaattttgatgtaaatgtcctg-------------------------------------------------
 || ||||| |||||  |||| ||||||||||| ||||||||||| || ||||| ||||||||||||||||||||||||||||||    || || ||  |||| | |   |||| | | |  || |||     |||  | ||| |   |  || | ||   |||||   || | ||   |                                                  
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatcctttttctgaattagtttgattcaaa-gtttttaagtaatcgttgctttgaca--tgcttccttcttgatga-gtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag

upper sequence: GLYMA05G32260.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ31182 (Selaginella moellendorffii), 5'ss of exon 3
GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcctaaactaaattgaataacccgtttgtcatttctctttgtccatacatttactttcggttaaataatgttgaattttgatgtaaatgtcctg
 || || || |||||  |    ||||||||||||||||||||||| || ||||| || |||||    ||||||||||||||     |||||||    |   |      || |     || |  || |  | | ||  |||||  ||   |         ||                 
AGTCTTCGAGAAGTCCTTCGCTTATGTGAAGCGCTTCAGCCGCTACAAGAATCCGGAGGCTGTCCAGCAAGTTCGAGAgtaaaaatctaaacttttctcgttccggttttggaagaatcacactgactttgcttt--ctttctcttcgttttcccctcgttccag-------------
















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|7591146|gb|AW706885.1|AW706885
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|15664606|gb|BI701977.1|BI701977
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|209729464|gb|BW651831.1|BW651831
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|192323976|gb|FK015697.1|FK015697
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|213604131|gb|DB974229.1|DB974229
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|9899186|gb|BE608084.1|BE608084
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|213591496|gb|DB955760.1|DB955760
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|120533986|gb|EH262119.1|EH262119
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|18718067|gb|BM523023.1|BM523023
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|5509484|gb|AI856042.1|AI856042
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|120534144|gb|EH262277.1|EH262277
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|9898920|gb|BE607888.1|BE607888
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|5509324|gb|AI855882.1|AI855882
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGATCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
EST: gi|192320820|gb|FK013910.1|FK013910
EST:     AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCCAGATATGAATTGGCTGAGTTTGAG
genomic: AAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcct ... tgacatacagAATTCTCGCCAGATATGAATTGGCTGAGTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGCTTCAGCCGCTATAAAAATCCCGATGCTGTTAGACAAGTTCGAGAgtatcctcctaaactaaattgaataacccgtttgtcatttctctttgtccatacatttactttcggttaaataatgttgaattttgatgtaaatgtcctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT