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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctctaaaagctagtaatttcaacattaggccatgtgtaaatttttcccacttatgatttccatcttaactgataaactttccccttttctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACACAGAGTATTCTTGGATATTGATATTGATAAACAGCGTTTAG

Basic information

species Glycine max
transcript GLYMA12G03540.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03540.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 1
tctctctaaaagctagtaatttcaacattaggccatgtgtaaatttttcccacttatgatttccatcttaactgataaactttccccttttctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACACAGAGTATTCTTGGATATTGATATTGATAAACAGCGTTTAG
     ||  ||  |  |  |   || | |     |    |  || |||||   |||| | || | |   |    ||  | || |    || || |  |  | || |  |      || ||||   ||||||||| |||||||||||| |||||||| ||||||||||| ||||||||| |||| | | |||
----actgcaattttttggtgataatactcccataaagatgcatctttcctttttatcaattacctgcaattgtattgatttac----ttactcaaatttgatgctagGGG----GAAGAGACGGCAGAAGAGGTGCCTGAAATTACTCACAGAGTGTTCTTGGATATCGATATTGATGAACAACATATAG
















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|213599098|gb|DB958359.1|DB958359
EST:     TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAG                         GTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
genomic: TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAGgtgcgccctt ... tctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
EST: gi|213605371|gb|DB966920.1|DB966920
EST:     TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAG                         GTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
genomic: TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAGgtgcgccctt ... tctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
EST: gi|151409297|gb|EV279105.1|EV279105
EST:     TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAG                         GTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
genomic: TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAGgtgcgccctt ... tctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
EST: gi|19452388|gb|BM953798.1|BM953798
EST:     TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAG                         GTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
genomic: TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAGgtgcgccctt ... tctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
EST: gi|9563823|gb|BE473332.1|BE473332
EST:     TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAG                         GTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
genomic: TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAGgtgcgccctt ... tctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
EST: gi|213617322|gb|DB965193.1|DB965193
EST:     TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAG                         GTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC
genomic: TCACATTTTCTGGTTCTACTACTACCAGTGGTTTTGCTACACCTCAACAGgtgcgccctt ... tctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcccacttatgatttccatcttaactgataaactttccccttttctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACACAGAGTATTCTTGGATATTGATATTGATAAACAGCGTTTAG
                                  ctttccccttttctga  CT-rich tract
        ttatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctctaaaagctagtaatttcaacattaggccatgtgtaaatttttcccacttatgatttccatcttaactgataaactttccccttttctgatgtagGTTGTTGAGATCATTGAGGAGAAACCAGAAGAGGAGCCTGAAATTACACACAGAGTATTCTTGGATATTGATATTGATAAACAGCGTTTAG

- - - - - - - - - - - - - - - - ccatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcccc