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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagacactagcttttgttcttgtgggttcattgttaggcgttttatgtgatgactgatgatgatgtttgtttgtttatcgattttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAGTGTTTGCCTCAAAGGATTGACCGTGAGAGCTTCCTCCTTGCACTTCACA

Basic information

species Glycine max
transcript GLYMA14G02500.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02500.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55120.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatagacactagcttttgttcttgtgggttcattgttaggcgtt--ttatgtgatgactgatgatgatgtttgtttgtttatcgattttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAGTGTTTGCCTCAAAGGATTGACCGTGAGAGCTTCCTCCTTGCACTTCACA
     |  |  || | ||| | ||  | ||  ||| |     | |  |||| |||  |||||        ||  |||                  ||||| ||||| ||||||||||||||||| ||||||||||| ||  || | || || || |||||||||||||| |   | ||| |  | ||||| ||||| |
-----gtaaggagttgttgcttttaggagtctattttcctttgctgattatctgagaactgaactcagaattcttttaac--------------gcagGTGAGTCCGATTGAGTATGGGCATGTGTTGCTGATTCCTCGTGTTCTTGATTGCTTACCTCAAAGGATTGATCACAAAAGCCTTTTGCTTGCTCTTCAAA
















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|10234213|gb|BE803101.1|BE803101
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTNTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|18040453|gb|BM308747.1|BM308747
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|11413203|gb|BF425214.1|BF425214
EST:     AAATGCTGCAGTTGATGTTGACAATTCTCCCAGCTTTTGT-GCCATCAAT                         GTTAGTCCTATTGAGTATGGGCATGATATGCTGATT
genomic: AAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTT-GTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATT
EST: gi|19346233|gb|BM891113.1|BM891113
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|6071672|gb|AW101059.1|AW101059
EST:     AAATGCTCCCAGT-GATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: AAATGCTCC-AGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|19452462|gb|BM953872.1|BM953872
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|208178799|gb|GD979606.1|GD979606
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTAGAAGTATGGGCAT
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATT-GA-GTATGGGCAT
EST: gi|13789523|gb|BG652114.1|BG652114
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|11687442|gb|BF595118.1|BF595118
EST:     TTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCTAG
genomic: TTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|9205432|gb|BE331656.1|BE331656
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|21994685|gb|BQ786213.1|BQ786213
EST:     GTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: GTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|19346232|gb|BM891112.1|BM891112
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|151406689|gb|EV276504.1|EV276504
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|7686123|gb|AW756771.1|AW756771
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|9203876|gb|BE330100.1|BE330100
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG
EST: gi|10234196|gb|BE803084.1|BE803084
EST:     CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAAT                         GTCAGTCCTATTGAGTATGGGCATGTNTTGCTGATTCCGCGCATTTTCGAG
genomic: CAAATGCTCCAGTTGATGTTGACAATTCTCCCAGCTTTGTTGCCATCAATgtatagacac ... ttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttttatgtgatgactgatgatgatgtttgtttgtttatcgattttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAGTGTTTGCCTCAAAGGATTGACCGTGAGAGCTTCCTCCTTGCACTTCACA
             gactgat  putative branch site (score: 3)
                                           ttttcgt  putative PPT
                               tttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagacactagcttttgttcttgtgggttcattgttaggcgttttatgtgatgactgatgatgatgtttgtttgtttatcgattttcgtaacagGTCAGTCCTATTGAGTATGGGCATGTTTTGCTGATTCCGCGCATTTTCGAGTGTTTGCCTCAAAGGATTGACCGTGAGAGCTTCCTCCTTGCACTTCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT