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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaattgtagtcactattattttgcaaataaaagtggtctacagcatcctgttaagtgaccaggctggaaattaatgtgttccatggctgtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCACTGAATCTTGGGCAGATGGACTCAAACTTGCCAGGGATATCAACTATCAG

Basic information

species Glycine max
transcript GLYMA16G17580.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 8
gcaaattgtagtcactattattttgcaaataaaagtggtctacagcatcctgttaagtgaccaggctggaaattaatgtgttccatggctgtac--atgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCACTGAATCTTGGGCAGATGGACTCAAACTTGCCAGGGATATCAACTATCAG
    ||   |   |  |  |      || ||  |    |||  | |||  || ||     | |   | | ||||||| |  ||  |  || ||    ||||||||||||||||| || ||||||||||||||||| || || ||||||||     | || ||||| || ||||| |||||||| |  | ||||||||| || 
-tctatcaaaaaaaacaaaaaaaaaaaagtatgaaccttct-tatcattttgctattcacctactgttggaattaattttctctctttctttattggtgcagTGAAGCAGATGAAATTTACAAAATATGCAGTGTTATGGGCAGTCCAACTTGGAATTCATGGGCTGAGGGACTTAAACTTGCTAATGCTATCAACTACCAA
















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|208167092|gb|GD962994.1|GD962994
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|193718080|gb|FK653378.1|FK653378
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGG
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGG
EST: gi|193495067|gb|FK460199.1|FK460199
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|208299186|gb|GE100085.1|GE100085
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|193599933|gb|FK550734.1|FK550734
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|208169630|gb|GD967787.1|GD967787
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATACGCAGTGTGATAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|193345679|gb|FK313762.1|FK313762
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTAACAAAA
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTA-CAAAA
EST: gi|193423617|gb|FK387282.1|FK387282
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCA
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCA
EST: gi|207727178|gb|GD701128.1|GD701128
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCTC
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|193377218|gb|FK341889.1|FK341889
EST:     TTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
genomic: TTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|193651862|gb|FK595565.1|FK595565
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCATCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|12690052|gb|BG156388.1|BG156388
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCAC
EST: gi|193411420|gb|FK381551.1|FK381551
EST:     GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAG                         TGAAGCAGATGAGATCTACAAAAT
genomic: GCTATAATGGCTGAGTTGTTCACTCTGCGTCCTCTATTCCCTGGTTCCAGgtaataactt ... gtacatgcagTGAAGCAGATGAGATCTACAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcctgttaagtgaccaggctggaaattaatgtgttccatggctgtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCACTGAATCTTGGGCAGATGGACTCAAACTTGCCAGGGATATCAACTATCAG
                         aattaat  putative branch site (score: 3)
                        aaattaatgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaattgtagtcactattattttgcaaataaaagtggtctacagcatcctgttaagtgaccaggctggaaattaatgtgttccatggctgtacatgcagTGAAGCAGATGAGATCTACAAAATATGCAGTGTGATAGGTAGTCCAACCACTGAATCTTGGGCAGATGGACTCAAACTTGCCAGGGATATCAACTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - -gtctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccaggct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggct