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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctcttaaactaaaattgaatgacccatttttcatttttctttgtccatgcatttactttcggttaaattatgttgaatgttgatctcaataccct...

Basic information

species Glycine max
transcript GLYMA03G22220.1
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: GLYMA03G22220.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G09920.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctcttaaactaaaattgaatgaccca---tttttcatttttctttgtccatgcat--ttactttcggttaaattatgttgaatgttgatc---tcaataccct------------------------------------------
 || ||||| |||||  |||| ||||||||||| ||||||||||| || ||||| |||||||||||||||||||||||||||||| ||   || || | |  |||  ||   ||||| | |  || |||      |||  || |||   | | | | |  ||  |   | |     | ||| |  |                                          
AGTGTTTGAGAAGTCCTTGCAATATGTGAAGCGATTCAGCCGCTACAAGAATCCAGATGCTGTTAGACAAGTTCGAGAgtatccttttt--ctgaattagtttgattcaaagtttttaagtaatcgttgctttgacatgcttccttcttgatgagtgagattttacagtcactggtttaattctatagttttgtgagaatatgctattccttaactcaacttttgcag
















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|254340129|gb|GR858254.1|GR858254
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|6964421|gb|AW433114.1|AW433114
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTGTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|192308232|gb|FK001302.1|FK001302
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|6718725|gb|AW306372.1|AW306372
EST:     GTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: GTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|208162826|gb|GD958938.1|GD958938
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|193512606|gb|FK471806.1|FK471806
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|192308233|gb|FK001303.1|FK001303
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|298185814|gb|HO030975.1|HO030975
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|4289246|gb|AI441448.1|AI441448
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|193389928|gb|FK357585.1|FK357585
EST:     AAGCGTTTCAGCCGCTATAAAA-TCCTGATGCTGTTAGACAAGTTCGAGA                         A-TTCTCGCAAGAATATCAATTGG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGA-TATCAATTGG
EST: gi|6964283|gb|AW432976.1|AW432976
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|208068170|gb|GD863682.1|GD863682
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|298168983|gb|HO020287.1|HO020287
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAGGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|298164053|gb|HO013698.1|HO013698
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAGGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|151409001|gb|EV278809.1|EV278809
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|193348188|gb|FK311104.1|FK311104
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAAGAATATCAATTGG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAA-GA-TATCAATTGG
EST: gi|193416036|gb|FK376670.1|FK376670
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|207820624|gb|GD791734.1|GD791734
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|193344828|gb|FK310404.1|FK310404
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
EST: gi|41145861|gb|CK606072.1|CK606072
EST:     AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGA                         AATTCTCGCAAGATATCAATTGGCTGAGTTTGAG
genomic: AAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctctt ... tcacatgcagAATTCTCGCAAGATATCAATTGGCTGAGTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATTTGAAAAGTCACTGCAGTATGTGAAGCGTTTCAGCCGCTATAAAAATCCTGATGCTGTTAGACAAGTTCGAGAgtatcctcttaaactaaaattgaatgacccatttttcatttttctttgtccatgcatttactttcggttaaattatgttgaatgttgatctcaataccct

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