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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctctacttgacttttctggtcaaacagagctgtttttcttcttttcctcagtccgtatactacgggccttaatatcatacttggtatgcatcttgcagAGGAACAAAAGGGATTTCTTTATTTTTATCTGCCTGGGAACTTTGACTTCTTCCCTTTCTGGTGCCGTTGCAGTTCAAA

Basic information

species Glycine max
transcript GLYMA07G30380.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G30380.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv03s0088g01260.t01 (Vitis vinifera), 3'ss of exon 10
-tgctctacttgacttttctggtcaaacagagctgtttttcttcttttcctcagtccgtatactacgggccttaatatcatacttggtatgcatcttgcagAGGAACAAAAGGGATTTCTTTATTTTTATCTGCCTGGGAACTTTGACTTCTTCCCTTTCTGGTGCCGTTGCAGTTCAAA
 |     | ||   | |      |  |   | | ||| ||  |||| | |    | | | |   |   |  | | |||  |  ||  ||| ||||||||||| ||||||| |||| |||||| ||||||||||||||||| ||||| |  | | | ||  || |   |||||||||||||
atatctgagtttgatctgagaccctgattaaccagttctttgtcttcttcctctttcct-tctcatcagtttcattattgtcattattattcatcttgcagAAGAACAAATGGGACTTCTTTGTTTTTATCTGCCTGGGAGCTTTGTCCACATTCATTGGTGCTATTGTTGCAGTTCAAA
















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|193422348|gb|FK389737.1|FK389737
EST:     TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG                         AGGAAACAAAA
genomic: TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAGgtaaggagtg ... catcttgcagAGGAA-CAAAA
EST: gi|193670139|gb|FK608651.1|FK608651
EST:     GGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTAGGGAAG                         AGGAACAAAAG
genomic: GGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTT-GGGAAGgtaaggagtg ... catcttgcagAGGAACAAAAG
EST: gi|193410793|gb|FK376360.1|FK376360
EST:     TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG                         AGGAACAAAAGGGATTT
genomic: TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAGgtaaggagtg ... catcttgcagAGGAACAAAAGGGATTT
EST: gi|193499891|gb|FK464248.1|FK464248
EST:     TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG                         AGGAACAAAAGGGATTTCTTTATTTTTATCTGCCTGGGAACTTTGACTTCT
genomic: TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAGgtaaggagtg ... catcttgcagAGGAACAAAAGGGATTTCTTTATTTTTATCTGCCTGGGAACTTTGACTTCT
EST: gi|193494762|gb|FK463590.1|FK463590
EST:     TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG                         AGGAACAAAAGGGATTTCTTTATTTTTATCTGCCTGGGAACTTTGACTTCT
genomic: TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAGgtaaggagtg ... catcttgcagAGGAACAAAAGGGATTTCTTTATTTTTATCTGCCTGGGAACTTTGACTTCT
EST: gi|193324203|gb|FK292609.1|FK292609
EST:     TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAG                         AGGAAACAAAAGGGATTT
genomic: TGGAACAGTTCGACCACCACTGTCCATGGATATCTAACTGTGTTGGGAAGgtaaggagtg ... catcttgcagAGGAA-CAAAAGGGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctcagtccgtatactacgggccttaatatcatacttggtatgcatcttgcagAGGAACAAAAGGGATTTCTTTATTTTTATCTGCCTGGGAACTTTGACTTCTTCCCTTTCTGGTGCCGTTGCAGTTCAAA
                       ccttaat  putative branch site (score: 4)
                         ttaatatcatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctctacttgacttttctggtcaaacagagctgtttttcttcttttcctcagtccgtatactacgggccttaatatcatacttggtatgcatcttgcagAGGAACAAAAGGGATTTCTTTATTTTTATCTGCCTGGGAACTTTGACTTCTTCCCTTTCTGGTGCCGTTGCAGTTCAAA

- - ctacttg
- - - - - - - tttctgg
- - - - - - - - - - -tcaaaca
- - - - - - - - - - - - - - - gctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccttaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtatg