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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaactttagcttattattattattattattattatcatgttactacttaccctttgtatgaatcttctcgtggtgcttattcaccaaaaaatcaa...

Basic information

species Glycine max
transcript GLYMA11G12260.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 11
lower sequence: AT4G39170.2 (Arabidopsis thaliana), 5'ss of exon 6
AACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaactttagcttattattattattattat-tatt-----atcatgttactacttaccctttgtatgaatcttctcgtggtgcttattcaccaaaaaatcaa
|  || || || |||||||| ||||| |||||||| |||||||||||||| ||  ||||||||    ||||    | |||     |     | |   || | ||| |  ||||   | | | |  |   || |   | |     |  |  ||   ||||     |  |||| ||||| |||  |                      
AGTTTTGCAGGTTATGATGAGTATGTTCCAATGGTTGACAAAGCTGTTGACGCCACCTGGAAGG-TTAAACCCACCGCCATCAACCGGGCTCCTTCTAAAGgtaatatttttatgctttcacttgtggcatcaaacactgggaaaagaaattgaaactttggtctcttatgtatcttttcgcag----------------------

upper sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 12
AACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaactttagcttat-tattattattattattattatcatgttactacttaccctttgtatgaatcttctcgtggtgcttattcaccaaaaaatcaa-
| ||| |  ||||||||||||||||| || ||||| ||||||||||||||||| |  |||||||| ||| |  | || || ||| ||    | || ||||||||  ||  |   ||||  |  ||  |  ||  ||  | |  |   | || |||   |    ||  | |   |        |  ||||    |  ||  | 
AGCTTCGGGGGGTATGATGAATATGTTCCCATGGTCGACAAAGCTGTTGATGCAGGTTGGAAGAAGCAAGCTGCTCTTCAAAGGCCTTCCTCATCCAAAGgttagtaagatctacttagatggtaaaaaaatggtttctgtttt-ccaatatttatgttcaacatttaccaatttact-ccttcgttcatgtgattattcat
















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|15288281|gb|BI472180.1|BI472180
EST:     TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
EST: gi|208118296|gb|GD920121.1|GD920121
EST:     TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
EST: gi|193321721|gb|FK287327.1|FK287327
EST:     TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAAACACCCCTGAAGGGATTCAAGCT
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAA-CACCCCTGAAGGGATTCAAGCT
EST: gi|208198503|gb|GD995538.1|GD995538
EST:     TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
EST: gi|193510644|gb|FK467142.1|FK467142
EST:     CGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
EST: gi|11687620|gb|BF595296.1|BF595296
EST:     TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
EST: gi|6964407|gb|AW433100.1|AW433100
EST:     TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
EST: gi|298172194|gb|HO021786.1|HO021786
EST:     TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
EST: gi|58015266|gb|CX702008.1|CX702008
EST:     TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC
genomic: TGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAACACCTCCCCTCCCTGACACTACAAACACCCCTGAAGGGATTCAAGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTTAGCTGGGTATGATGAATATGTACCAATGGTGGACAAAGCTGTTGATGCTGCCTGGAAGAACCAAACATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaactttagcttattattattattattattattatcatgttactacttaccctttgtatgaatcttctcgtggtgcttattcaccaaaaaatcaa

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC