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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagggttgttatttttctattatatcagagaacactacatgcttcacttccgagacagacaaatataaacttttttcgattttcttgttttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACAATTTCGAGACAAGGCAGCTTCATCCAGATCAATGACT

Basic information

species Glycine max
transcript GLYMA04G31180.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv17s0000g04690.t01 (Vitis vinifera), 3'ss of exon 6
tacagggttgttatttttctattatatcagagaa-cactacatg-cttcacttccgagacagacaaatataaacttttttcgatttt-cttgttttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACAATTTCGAGACAAGGCAGCTTCATCCAGATCAATGACT
 |      | ||  |||   | |   |  | |   | ||  ||| ||||   |   | |    | |||    | |     | |      ||| |||||  |||||||||||||||||| || |||||||| ||||| ||| |||| |||||||||||||| || ||||| ||||  || ||||||||| ||
-aagctccttttgctttagcactcagtttgtgcttctctgtatggcttcttgtttcatatgatccaatcactaataaaaacaaccaagtttgatttgg--cagACCAGATGAAGCAGAACTCTTTGCCAAGTCTGCCCAGAATGCATATAAACAATTTCGTGATAAGGCGGCTTTTTCAAGATCAATGGCT

upper sequence: GLYMA04G31180.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv17s0000g04700.t01 (Vitis vinifera), 3'ss of exon 2
tacagggttgttatttttctattata-tcagagaacactaca-tgcttcacttccgagacagacaaatataa--acttttttcgattttcttgttttggt--acagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACAATTTCGAGACAAGGCAGCTTCATCCAGATCAATGACT
       || |  |||  || |   | ||||      || |  ||  |  ||||            ||  ||  |||  |   ||    |  ||||   |   |||||||||||||||||| || |||||||| |||||   | |||| |||||||||||||| |||||| | ||||  || ||||||||| ||
------cttttcctttccctgtagcactcagtttgtgcttctctgtatggcttcttgtttcatatgatccaatcactaataaagacaaccaagtttgatttggcagACCAGATGAAGCAGAACTCTTTGCCAAGTCTGCCTGGAATGCATATAAACAATTTCGCGACAAGACGGCTTTTTCAAGATCAATGGCT
















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|10846715|gb|BF069541.1|BF069541
EST:     TCAAGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAG                         ACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
genomic: TCAAGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAGgtaaatattg ... tttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
EST: gi|58022499|gb|CX709240.1|CX709240
EST:     CAAGGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAG                         ACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
genomic: CAA-GGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAGgtaaatattg ... tttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
EST: gi|209710229|gb|BW658925.1|BW658925
EST:     TCAAGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAG                         ACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
genomic: TCAAGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAGgtaaatattg ... tttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
EST: gi|58014942|gb|CX701684.1|CX701684
EST:     TCAAGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAG                         ACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
genomic: TCAAGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAGgtaaatattg ... tttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
EST: gi|21889311|gb|BQ742524.1|BQ742524
EST:     TCAAGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAG                         ACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA
genomic: TCAAGGGGAAGATATGCTGAGCTCCTTGCTGCTGAGCAACGTCCTTTCAGgtaaatattg ... tttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttccgagacagacaaatataaacttttttcgattttcttgttttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACAATTTCGAGACAAGGCAGCTTCATCCAGATCAATGACT
                          cttttttcgattttct  CT-rich tract
                 aaatataaactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagggttgttatttttctattatatcagagaacactacatgcttcacttccgagacagacaaatataaacttttttcgattttcttgttttggtacagACCAGATGAAGCAGAGCTATTTGCCAAATCTGCTCAGCATGCTTATAAACAATTTCGAGACAAGGCAGCTTCATCCAGATCAATGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - gggttgt
- - - - - - - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - - - - cacttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatataa