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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCATCAAACGAAAAATTGTGCAAGCTGCATCTATCGATTTACAGTCTCGGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTGgtgagttgtttcagcaaattttcatcccctcgctttctctccttgtaaattatactttctgtattgaaaatggttgttttcaatgaaatgcttgaatttt...

Basic information

species Glycine max
transcript GLYMA07G40240.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40240.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv12s0035g01830.t01 (Vitis vinifera), 5'ss of exon 7
GGCCATCAAACGAAAAATTGTGCAAGCTGCATCTATCGATTTACAGTCTCGGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTGgtgagttgtttcagcaaattttcatcccctcgctttctctccttgtaaattatactttctgtattgaaaatggttgttttcaatgaaatgcttgaatttt-----
||| |||||| | || ||||  || |||||  | |  || || || || || ||| |||| |||||||||||||||||  ||||||||||||| ||||||||| || |    ||  | | ||||     || |  | |    ||| ||    |     ||  ||| |||    |||  |   ||| | | ||       |     
GGCAATCAAAAGGAAGATTGCACAGGCTGCTGCCACTGACTTCCAATCACGAAGTTTACCAGCAAAGCTTCGTATAGAACCTGATGATCCTGAAGATGTGgtgggtgg----agttactattcaaattttcaccattttcttttggaatgagttacagctaaattaaaagcc-ttgcataggatgcatttctcttgccattatga
















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|254323191|gb|GR835799.1|GR835799
EST:     GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTG                         AAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
genomic: GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTGgtgagttgtt ... ataatcacagAAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
EST: gi|9820674|gb|BE556184.1|BE556184
EST:     GAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCCTGAG-ATGTG                         AAAGCTTCGAAACGCA-GAAA-TACATGCCTTTA-GTCAAAGATGCCGATG
genomic: GAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCC-TGAGGATGTGgtgagttgtt ... ataatcacagAAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
EST: gi|151393165|gb|EV263040.1|EV263040
EST:     GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTG                         AAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
genomic: GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTGgtgagttgtt ... ataatcacagAAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
EST: gi|37995015|gb|CF806604.1|CF806604
EST:     GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTG                         ----CTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
genomic: GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTGgtgagttgtt ... ataatcacagAAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
EST: gi|192334366|gb|FK025543.1|FK025543
EST:     GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAG-ATGTG                         AAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAA-GATGCGGATG
genomic: GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTGgtgagttgtt ... ataatcacagAAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
EST: gi|192334367|gb|FK025544.1|FK025544
EST:     GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTG                         AAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG
genomic: GGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTGgtgagttgtt ... ataatcacagAAAGCTTCGAAACGCAAGAAAATACATGCCTTTAAGTCAAAGATGCGGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCATCAAACGAAAAATTGTGCAAGCTGCATCTATCGATTTACAGTCTCGGAGTCTACCTGCAAAGCTTCGTATAGAGGCTGATGATCCTGAGGATGTGgtgagttgtttcagcaaattttcatcccctcgctttctctccttgtaaattatactttctgtattgaaaatggttgttttcaatgaaatgcttgaatttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG