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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttatacaatttgtttactttttcttgtgctaggtttctatttcctgtgtaactattaacccattgatatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG

Basic information

species Glycine max
transcript GLYMA11G06250.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G081915_T01 (Zea mays), 3'ss of exon 2
---------------------------------------gttcttatacaat-ttgtttact--ttttcttgtgctaggtttctatttc-ctgtgt------aactattaac-ccattgatatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG
                                        | ||  | |  | ||||  |||  ||    | |||     | ||  ||| |||         |||| | ||  ||  |  |   |  ||||| |||||||| || |||||||||||||| |||||||||||||| ||| | |||
gtccgtctttctctcgctatcatcgaccctgcttgcttgctgctcgtgctgtcttgtgcactaattgctatctgcgccactcctgcttcactggactaatcaaactgtcaaagcccctttttcatttcagGCGCGTTTCTTTTTCCAACAACTCATATCAGGGGTCAGCTACTGCCATTCCATG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G066867_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------gttcttatacaatt-tgtttactttttcttgtgctaggtttctatttcctgtgtaactattaacccattgata--tgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG
                                                            ||| | |  | || || | ||  |         ||    |  |      ||  |   || || |  |  |    | |  ||||| |||||||| || || ||||||||||| |||||||||||||| ||| | |||
gtccattccttttctttcgtcttctctcgctttcatcaacgctgcttgctcgtgctgcctttcctctgtacttgtgatgacactcctgccctgtacaactacaaacatggtacactaatcaaactgtcaaagcttctttcagGCGCGTTTCTTTTTCCAGCAACTCATATCAGGGGTCAGCTACTGCCATTCCATG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 3
gttcttatacaatttgtttactttttcttgtgctaggtttctat-ttcctgtgtaactattaacccattgatatgtc-----acagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG
            || | ||    ||| | || ||  |||    | ||  ||||| |||| | | |  |   | | |      | ||||||| ||||||||||| || || |||||||| || ||||| ||||||||||||
----------gtttggattctgatttatcgtactgtgttgtggtattgatgtgtgactactgatctttaagtttttttatgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG

upper sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 3
gttctt-atacaatttgtttactttttcttgtgctaggtttc-tatttcctgtgtaactattaacccattgatatgtc-acagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG
|||||| || |||    ||   |||||  | | |||| |||  |  |   |   |   |  |   |  | | |   ||  |||||||| || ||||||||||| || ||||| ||||||||||| ||||||||||||
gttcttgattcaacccattgggttttttcttttctagtttttgtgctatttccatggtttcttgacactggttgcttctgcagGCTCGCTTTTTCTTTCAACAGCTTATATCAGGGGTCAGCTATTGTCATGCAATG

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|22931738|gb|BU548877.1|BU548877
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
EST: gi|213618240|gb|DB973010.1|DB973010
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTCA-CAACTCATATCTGGNGTCAGCTACTGTCATGCA
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
EST: gi|9258485|gb|BE346632.1|BE346632
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
EST: gi|254317661|gb|GR826645.1|GR826645
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
EST: gi|14259137|gb|BG882045.1|BG882045
EST:     GAGACCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTTC-TTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTCCTGTCATGC
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCT-CGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGC
EST: gi|14259185|gb|BG882093.1|BG882093
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTCA
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTCA
EST: gi|19348943|gb|BM893475.1|BM893475
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
EST: gi|209714671|gb|BW674234.1|BW674234
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTC
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTC
EST: gi|7684855|gb|AW755503.1|AW755503
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCANGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
EST: gi|209697502|gb|BW670003.1|BW670003
EST:     GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAG                         GCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA
genomic: GAGAGCTATTTGAGAAAATCTGCAATGCAGGGCATTTTAATGAGGATGAGgttcttatac ... tatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtgctaggtttctatttcctgtgtaactattaacccattgatatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG
                           taactattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttatacaatttgtttactttttcttgtgctaggtttctatttcctgtgtaactattaacccattgatatgtcacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT