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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttcttttccccatagaaggacatttgtgtttttggaaatttaggcttgctatatttgatgctgaacctctatgatgctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTC

Basic information

species Glycine max
transcript GLYMA11G11490.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11490.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 14
gtatggttcttttccccatagaaggacatttgtgtttttggaaatttaggcttgctatatttgatgc---tga-acctctatgatgctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTC
||||| ||||| ||   ||  |   |  ||  ||     ||   |||    ||||| ||||| || |   |||   ||   |  ||   |||||||||||| |  ||||||||||||||||  |||||||| ||||| |||||||| || || || ||||| ||||||||  |||| |||||||| |||||||| |
gtatgcttcttctctggatttacaaa-gttgatgcaa--gggggttttattttgctttatttcattcatatgatgtcttgtttctgaccttttcagTTACTTGAGATTATGGGAGAATTCAACCCAGAGCAGCAGCGGGCCTTCTGCCAGTTCGTCACTGGCGCACCTAGACTGCCGCCTGGTGGTCTGGCAGTGC

upper sequence: GLYMA11G11490.2 (Glycine max), 3'ss of exon 14
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 14
gtatggttcttttccccatagaaggacatttgtgttt--ttggaaatt-----------taggcttgctatatttgatgctgaacct-----ctatgatgctatt----ttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTC
||| | |||||       | |  || ||||||  |||  | |||||             ||    |  ||||||   |||   |  |      | | ||||  ||    |  ||||||| | ||| |||||||||||||| || ||||| |||| ||| ||||| |||||  ||||||||||||||||| | |||||||| || |||||| |  
gtaagattcttcctatatttg--gggcatttggatttagtgggaaacagggtgtaatgataactcttatatattgactgcatgatttgtttattgtaatgcctttgctttctagTTACTTGAAATCATGGGAGAATTCACTCCTGAGCAGCAGCATGCATTCTGCCAATTCATTACTGGTGCACCTAGGCTTCCTCCTGGAGGTCTGGCAATGT
















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|17400311|gb|BM177093.1|BM177093
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatggttct ... ctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
EST: gi|7028762|gb|AW458545.1|AW458545
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatggttct ... ctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
EST: gi|11275017|gb|BF325341.1|BF325341
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatggttct ... ctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
EST: gi|15814707|gb|BI786982.1|BI786982
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatggttct ... ctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
EST: gi|23732846|gb|BU764597.1|BU764597
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatggttct ... ctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
EST: gi|208175474|gb|GD976869.1|GD976869
EST:     ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
genomic: ATATAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatggttct ... ctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
EST: gi|10843371|gb|BF066672.1|BF066672
EST:     TAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAAT                         TTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT
genomic: TAAAATTTGACCATGGTTATACTGCCAAGAGCCCTGCCATAGTTAATgtatggttct ... ctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaaatttaggcttgctatatttgatgctgaacctctatgatgctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTC
                     atttgat  putative branch site (score: 5)
                                             ctattttc  putative PPT
                  tatatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggttcttttccccatagaaggacatttgtgtttttggaaatttaggcttgctatatttgatgctgaacctctatgatgctattttcagTTACTCGGAATTATGGGAGAATTCACACCAGAGCAACAGCGTGCCTTCTGTCAATTTGTTACTGGTGCACCTAGGTTGCCTCCTGGTGGACTGGCAGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA