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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTCTCCACATGCTCTTCACATCTCTGACTGTTTGGATGACTTGAGACCTGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATGgtatgtctcagccttgttcacttgttggactaatttattaattatctccactaaatggttcaatcatacttttgtcaagaactaatattaatattaaatttggtcatgatatatatgcattggattattttgattgaataatttttgaggtgttttattgtag

Basic information

species Glycine max
transcript GLYMA03G28210.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G28210.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G130348_T01 (Zea mays), 5'ss of exon 3
ACTTCTCCACATGCTCTTCACATCTCTGACTGTTTGGATGACTTGAGACCTGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATGgtatgtctcagccttgttcacttgttggactaatttattaattatctccactaaatggttcaatcatacttttgtcaagaactaatattaatattaaatttggtcatgatatatatgcattggattattttgattgaataatttttgaggtgttttattgtag
||   | | ||||  || |||| |||||||||  || ||||  |  | || || || ||||| ||||||||||||||||| ||||||||||| || || |||||||  | |       ||   |     ||   || | |   ||     ||||    | | |||  |   | |   || | || | ||  | || |||  |   ||  | | |   ||||     | ||  || | ||  ||                    
ACCCTTGCGCATGACCTGCACACCTCTGACTGCCTGCATGAGCTCCGGCCCGGCGACCACATCGAGATTCAGTGGAGAAGGAACAAAGAATTCCCATACGgtatgttcccgagccaccca---gcaacgcttgcttttaatgcattgatgctaa----tcctatccgatagtggctgaggagtattttt--tttttaatcagtggatagtgtgttctcattcatgcacttccat-gcatgtttggcag---------------

upper sequence: GLYMA03G28210.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0040g01290.t01 (Vitis vinifera), 5'ss of exon 3
ACTTCTCCACATGCTCTTCACATCTCTGACTGTTTGGATGACTTGAGACCTGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATGgtatgtctc--agccttgtt--cacttgttggactaatt-tattaattatctccactaaatggttcaatcatact-tttgtcaa--gaactaatattaa----tattaaatttggtcatgata-tatatgcattggattattttgattgaataatttttgaggtgttttattgtag-------------
  | |||| |||| ||||||  |||||||||||||  |||| || | ||| || ||||| ||||||||||| ||||| | ||||||||| || ||||| |||  |||    | || |  |  ||    | ||  | |||  |||     | |   | |||   ||     || || || |  ||  |  |  | || |     ||   ||      |||| || | |||||    | ||| ||    | |   ||     ||||| ||  || |               
GTTCCTCCTCATGTTCTTCATGTCTCTGACTGTTTAAATGATTTAAAACCAGGGGATCATATTGAGATTCAATGGAGGAAAAACAAAGAGTTGCCTTACGgtgcgtcctcaaaccatcatagcatccctggggttcattgcatttggcctgttttcaaaagcttttgtatatgctattcgataactgtgcccacatcatcttctacagaacaaatacatgttactgtatgctaatgtttacttgtgattatggatgaacaaggtgattgtttttgctaaatgtttgcag
















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|14259166|gb|BG882074.1|BG882074
EST:     TGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATG                         GTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
genomic: TGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATGgtatgtctca ... tttattgtagGTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
EST: gi|58024860|gb|CX711601.1|CX711601
EST:     TGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGATTTTCCTTATG                         GTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
genomic: TGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATGgtatgtctca ... tttattgtagGTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
EST: gi|11275131|gb|BF325454.1|BF325454
EST:     TGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATG                         GTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
genomic: TGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATGgtatgtctca ... tttattgtagGTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
EST: gi|11274180|gb|BF324548.1|BF324548
EST:     AAGAAACAAAGAATTTCCTTATG                         GTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
genomic: AAGAAACAAAGAATTTCCTTATGgtatgtctca ... tttattgtagGTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
EST: gi|192306507|gb|FG997205.1|FG997205
EST:     TGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATG                         GTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA
genomic: TGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATGgtatgtctca ... tttattgtagGTTGGTGGTATGGTGTCATTGGTCATTTGGAACAATGTCAAGGACATGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTCTCCACATGCTCTTCACATCTCTGACTGTTTGGATGACTTGAGACCTGGAGATCACATTGAGATTCAGTGGAGAAGAAACAAAGAATTTCCTTATGgtatgtctcagccttgttcacttgttggactaatttattaattatctccactaaatggttcaatcatacttttgtcaagaactaatattaatattaaatttggtcatgatatatatgcattggattattttgattgaataatttttgaggtgttttattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA