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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatatccttctgaagtttggtaaaagcttttagggccctatgaaattcctgatcacagcagttctatgacctcacttttatggatggtttgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCATCTAAAGGAATGTTCATAGACTCTTGCTATGCCCACTGCCAAACTGAAAT

Basic information

species Glycine max
transcript GLYMA09G35050.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G35050.4 (Glycine max), 3'ss of exon 11
lower sequence: Vv02s0087g00400.t01 (Vitis vinifera), 3'ss of exon 11
------tcatatccttctgaagtttggtaaaagcttttagggccctatgaaattcctgatcacagcagttctatgacctcacttttatggatggtttgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCATCTAAAGGAATGTTCATAGACTCTTGCTATGCCCACTGCCAAACTGAAAT
| | |||| | | | | | ||| | | | | | | || | | | |||| | | ||| || ||| |||||| | ||| | || || || | | || ||| | || ||||||||||||||| |||| |||||||||||||||||||| |||||
cttggcttgtttcctacct--gcccgttttgggttttctg----caacaacaaccatgtctttgaggactaatcgtttttggtttttttttttttttctttctcagATTTCAGGGTGCAGTTTCTTAGTGCAATCAAAGGACTGATAGGCTCCCCCTCCAAAGGAATGTTCATAAACTCCTGCTATGCCCACTGCCAAACCGAAAT
















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|10709683|gb|BF009407.1|BF009407
EST:     CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAG                         GCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
genomic: CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAGgtgaatattc ... tgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
EST: gi|37995321|gb|CF806910.1|CF806910
EST:     CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAG                         GCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
genomic: CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAGgtgaatattc ... tgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
EST: gi|7589608|gb|AW705379.1|AW705379
EST:     CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAG                         GCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
genomic: CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAGgtgaatattc ... tgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
EST: gi|15285962|gb|BI469853.1|BI469853
EST:     CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAG                         GCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
genomic: CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAGgtgaatattc ... tgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
EST: gi|33389751|gb|CA852958.1|CA852958
EST:     CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAG                         GCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT
genomic: CAAGCTTGATATAAACAACTGCTCACCTGATCAACTTGATCTAATGCAAGgtgaatattc ... tgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcctgatcacagcagttctatgacctcacttttatggatggtttgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCATCTAAAGGAATGTTCATAGACTCTTGCTATGCCCACTGCCAAACTGAAAT
                                           tttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatatccttctgaagtttggtaaaagcttttagggccctatgaaattcctgatcacagcagttctatgacctcacttttatggatggtttgatttacagGCTTCAGGACAGAATTTTTAAGGGCTATAACTGTGCTAGGCAACTCTTCATCTAAAGGAATGTTCATAGACTCTTGCTATGCCCACTGCCAAACTGAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA