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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaatttgcacttacgtatttatgaataagaattggaatttcatgtttgtgtcctgtaacacagtccattcctctcgttgatcctatgtctgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATTAAAATCCCAGCTTCAAAATCCATATGGGCAAGGTTGCTATTCATTCTCC

Basic information

species Glycine max
transcript GLYMA17G35410.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G35410.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G27750.1 (Arabidopsis thaliana), 3'ss of exon 7
--ggaatttgcacttacgtatttatgaataagaattggaatttcatgtttgtgtcctgtaacacagtccattcctctcgttgatcctatgtctgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATTAAAATCCCAGCTTCAAAATCCATATGGGCAAGGTTGCTATTCATTCTCC
       |  || || |  |    ||||| |  ||   |   |  ||| |   | |   || | | |  |   || ||    |  || | ||||  | | || | || ||||||||| |||||||||||||||| |||||||| || || || || ||||| || ||||   |||| |||||||||   || |||||||| |
gtatgtgtcacattttcaaaccc-tgaatcatcataacaccattttgtcttcctacgtaaatataat--aactctatcaa-aactctctttctggtggc-agCTCCAAGATTTCATAACATACTTGAAGCAGAGAGATTGTGCAGGAGTAATAAAGATCCCTGCATCAAGTCCCATGTGGGCAAGGCATCTCTTCATTCTTC

upper sequence: GLYMA17G35410.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv18s0001g09200.t01 (Vitis vinifera), 3'ss of exon 7
-ggaatttgcacttacgtatttatgaataagaattggaatttcatgtttgtgtcctgtaacacagt-ccattcctctcgttgatcctatgtctgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATTAAAATCCCAGCTTCAAAATCCATATGGGCAAGGTTGCTATTCATTCTCC
  | |  |||||||   |  | |  | | |  |    | | |||  ||| |    ||||| ||  | |  | | | |   |      |  | | |    |||||||||||||||||| |||||||||||||||||||||| || || || ||||| || ||||||   ||||| || ||||||||| | || || ||||| |
atgtacatgcacttctttgctgagcattcatgacc--agtatcaattttataaattgtaagacgttgctgtacattttaattgatgcaaatgtattcttcagTTTCAGGATTTCATAGCATACTTGAAGCAGAGGGATTGCGCAGGAGTAATTAAGATTCCAGCTGTGAAATCAATGTGGGCAAGGCTACTCTTTATTCTTC
















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|17963168|gb|BM269920.1|BM269920
EST:     AGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGG                         TTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
genomic: AGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGGgtatgttttc ... tgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
EST: gi|19270973|gb|BM887229.1|BM887229
EST:     AGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGG                         TTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
genomic: AGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGGgtatgttttc ... tgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
EST: gi|193355617|gb|FK322960.1|FK322960
EST:     AGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAGAAGG                         TTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
genomic: AGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGGgtatgttttc ... tgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
EST: gi|6454744|gb|AW185427.1|AW185427
EST:     AGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGG                         TTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
genomic: AGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGGgtatgttttc ... tgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
EST: gi|22928227|gb|BU545366.1|BU545366
EST:     GAAGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGG                         TTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT
genomic: GAAGGGAAGTGTGCCGTTTGATTCCATCTTCCTCTAGTGACCACAAAAGGgtatgttttc ... tgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaatttgcacttacgtatttatgaataagaattggaatttcatgtttgtgtcctgtaacacagtccattcctctcgttgatcctatgtctgtcgaccagTTTCAGGATTTCATATCATACTTGAAGCAGAGGGATTGTGCTGGGGTTATTAAAATCCCAGCTTCAAAATCCATATGGGCAAGGTTGCTATTCATTCTCC

- - - - cacttac
- - - - - - - - - - - - aataagaa
- - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - -tcctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtc