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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttttgcttcccttcatttggaaccttttatcacccctttttaatttcctccgtatttatccgttgcaatctttaatttgcaattatttactgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAGCATTGCTCAGTCTGGGTGTCTGACAGTCAGTCTTGTCGTCTTCTATGTT

Basic information

species Glycine max
transcript GLYMA11G36990.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G36990.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 9
agttttgcttcccttcatttggaaccttttatcacccctttttaatttcctccgtatttatccgttgcaatctttaatttgcaattatttactgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAGCATTGCTCAGTCTGGGTGTCTGACAGTCAGTCTTGTCGTCTTCTATGTT-----------
        |||   |  ||| |    |  | ||  |  |||  |||||  |     ||   || |||||  | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||| |||||| || ||||||||||| | ||||||||||| |||||||| |||| ||| | ||||            
--------ttcgaatggttttgt-tttcctgtc-tcgttttccaattttatattgcttctacctttgcatccattaatttgcaattatctactgttccagtgagtactagGACATGTTTGAGGGTTGAGAAGGTCCAGGGTTGTCGTCCAGCATTGCTCAATATGGGTGTCTGAAAGTCAGTCGTGTCATCT-CCATGTCGCAGCGCTTGT
















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|15661571|gb|BI698942.1|BI698942
EST:     CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|208052191|gb|GD853476.1|GD853476
EST:     AGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: AGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|6501895|gb|AW203268.1|AW203268
EST:     CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|207688765|gb|GD671284.1|GD671284
EST:     CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|18717828|gb|BM523005.1|BM523005
EST:     CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
EST: gi|207837324|gb|GD806144.1|GD806144
EST:     AGATCAAAATGTATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAA
genomic: AGATCAAAATG-ATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAA
EST: gi|6913500|gb|AW395030.1|AW395030
EST:     CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAG                         TGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG
genomic: CGGCTGAGTCTGAAGAATCTCCTTCATCAGCTGCAGATCAAAATGATCAGgtttgttgtg ... actgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctccgtatttatccgttgcaatctttaatttgcaattatttactgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAGCATTGCTCAGTCTGGGTGTCTGACAGTCAGTCTTGTCGTCTTCTATGTT
                          ctttaat  putative branch site (score: 4)
                                              ctgttcc  putative PPT
                       aatctttaatttgcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttttgcttcccttcatttggaaccttttatcacccctttttaatttcctccgtatttatccgttgcaatctttaatttgcaattatttactgttccagTGAGTACTAGGACATGTTTGAGGGTTGAGAAGGTCCAGAGTTGTCATCAAGCATTGCTCAGTCTGGGTGTCTGACAGTCAGTCTTGTCGTCTTCTATGTT

- - - -cttccct
- - - - - - - - - - - - - - - - - ccccttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgcaa