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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccccttcctccaattcaagaactggttatagttgaggaggtccttgaggattattttctcataaggttaggaaatcttatatgcatgctgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCAGAGGCATTTTGGTGTTTTGTTGCTCTAATGGAACGTCTCGGACCCAATT

Basic information

species Glycine max
transcript GLYMA17G12070.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12070.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G52580.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------------------------------------------------------------------ctcccctt--cctccaattcaaga--actgg------ttatagttgaggaggtccttgaggattattttctcataa--ggttaggaaatcttatatgcatgctgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCAGAGGCATTTTGGTGTTTTGTTGCTCTAATGGAACGTCTCGGACCCAATT
                                                                                          | || |||  | | |||  ||  |   ||||      || || ||  ||   |   |  | ||| ||   |  |       |   |||| || | |  || ||| ||   ||||||||||||||  ||| ||||| || ||||| ||||||||  ||||||||||  | ||||||||||| || || || |||||||| || |||||||| |
gtactcatcagttttcaaagttcattcttagcactgaattacaagttggcgttgtccttactgttatgaatccatattttgggtcggttgccccacttagcgtacaaaacagaactgctggacactcttctatttctggcttttgctttgaatttttccattgtgtttaactgacaaatgtt-tttttat-ctggttgttagGGAATGAGTGATTATCTGTCTCCTATCTTGTTCGTGATGGAGGATGAATCAGAATCTTTTTGGTGTTTCGTGGCACTGATGGAACGACTTGGACCCAACT
















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|5509199|gb|AI855757.1|AI855757
EST:     ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAG                         AGAATGAGTGATCATCTATCTACAATATTGTTTGTGATGGATAATGAATCA
genomic: ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAGgtaactatgc ... tgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA
EST: gi|9260051|gb|BE348198.1|BE348198
EST:     ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAG                         GGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA
genomic: ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAGgtaactatgc ... tgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA
EST: gi|16348998|gb|BI974593.1|BI974593
EST:     ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAG                         GGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA
genomic: ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAGgtaactatgc ... tgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA
EST: gi|7591273|gb|AW707009.1|AW707009
EST:     ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAG                         GGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA
genomic: ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAGgtaactatgc ... tgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA
EST: gi|17153534|gb|BM143467.1|BM143467
EST:     ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAG                         GGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA
genomic: ATATCCTGTTGACATATTCATTCTACAACTTTGATCTTGGTTATTGCCAGgtaactatgc ... tgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaggattattttctcataaggttaggaaatcttatatgcatgctgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCAGAGGCATTTTGGTGTTTTGTTGCTCTAATGGAACGTCTCGGACCCAATT
                                            ctgtttt  CT-rich tract
      attattttctcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctccccttcctccaattcaagaactggttatagttgaggaggtccttgaggattattttctcataaggttaggaaatcttatatgcatgctgttttacagGGAATGAGTGATCTTCTATCTCCAATATTGTTTGTGATGGATAATGAATCAGAGGCATTTTGGTGTTTTGTTGCTCTAATGGAACGTCTCGGACCCAATT

ctcccct
- - - -tcctcca
- - - - - - - - - - - actggtt
- - - - - - - - - - - - - - - - - -gaggagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgc