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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatctaagttttgtcaaacttttatttttttaatgcaattgaggattgagattacaattttggatgatctgggttgtgaattatggtttctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATCAGAGCTCAAGTCACCACTGAGGCTCCAGCCAAGGTTGAAAAAGAGTCCA

Basic information

species Glycine max
transcript GLYMA16G23710.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23710.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 3'ss of exon 1
tttatctaagttttgtcaaacttttatttttttaatgcaattgaggattgagattacaattttggatgatctgggttgtgaattatggtttctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATCAGAGCTCAAGTCACCACTGAGGCTCCAGCCAAGGTTGAAAAAGAGTCCA
                      | ||  | | || |   ||    ||||| |||| | |  |   || || ||||      |||||  ||  ||   |||| | | |||   ||||||||| | | |  | |||| || || ||||| |||||||| || ||||||||||||||||| |||||||| || ||    ||||
-------------------gtatataaatgtctactcacat----gattg-gatt-ccacatcaaat-atttgggcaagttattatt-ttgtttgtgcagGTTCCTTTGTTTTACAGAGATATCTCTGCCGGTGGGAGAGTGGTTTCTATCAGAGCCCAGGTCACCACTGAGGCTCCTGCCAAGGTCGAGAAGATTTCCA
















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|213595158|gb|DB972092.1|DB972092
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|11688404|gb|BF596080.1|BF596080
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|12774303|gb|BG239230.1|BG239230
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|120532662|gb|EH260795.1|EH260795
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|209724751|gb|BW651482.1|BW651482
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|120529657|gb|EH257791.1|EH257791
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|213611575|gb|DB960855.1|DB960855
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|213600291|gb|DB955873.1|DB955873
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|105634481|gb|DW247568.1|DW247568
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|209707438|gb|BW670951.1|BW670951
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|213592264|gb|DB965999.1|DB965999
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|213597976|gb|DB972164.1|DB972164
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|6667179|gb|AW278638.1|AW278638
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAC                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
EST: gi|209718136|gb|BW657795.1|BW657795
EST:     TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAG                         GCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC
genomic: TCCCAAGCAGGACCTCCATCATTACCCCAGAGAGAGTTGTATTCAAGAAGgtattgtttc ... tctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgagattacaattttggatgatctgggttgtgaattatggtttctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATCAGAGCTCAAGTCACCACTGAGGCTCCAGCCAAGGTTGAAAAAGAGTCCA
                                           tttctttctc  CT-rich tract
       attacaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatctaagttttgtcaaacttttatttttttaatgcaattgaggattgagattacaattttggatgatctgggttgtgaattatggtttctttctcagGCTTCATTGCAATACAGAGATGTTTGTAGCAGTGGAAGGGTAGTTTCCATCAGAGCTCAAGTCACCACTGAGGCTCCAGCCAAGGTTGAAAAAGAGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - -tcaaact
- - - - - - - - - - - - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttgtg