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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccttacctttcattcttcccttttgcagtttgttagaattgagtgagtgagggtgtatgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGAGTTCAGGTTGAAGTGGG

Basic information

species Glycine max
transcript GLYMA20G36050.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36050.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G64720.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacgccttacctttcattcttcccttttg---cagtttgttagaattgagtgagtgagggtgtatgct-tgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGAGTTCAGGTTGAAGTGGG
|||| ||   || | | | |||    |||     |   ||||         ||| | |   | | |    ||  ||| ||| || || |||||||| |||||||| ||||| || || || | ||| ||| |||| ||||| ||||||||||||||||||||| | |  |||||||
gtacccccctccctccttcctttaagtttagtttaacatgttcctccaagttgaatcattttttgtatgatgccagAATGGGCCTCCCCAGTACCGTAGCAGAACTGTGTTTGAGGATGCCACTCCCGAGATGGTCAGGGACTTCTTTTGGGATGATGAGTTCCGTTCCAAGTGGG

upper sequence: GLYMA20G36050.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g02820.t01 (Vitis vinifera), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------gtacgccttacctttca----ttcttcccttttgcagtttgttagaattgagtgagtgagggtgtat---gcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGAGTTCAGGTTGAAGTGGG
                                                                                                     |   ||  ||  ||  |    |  ||   |||   |  ||||    ||||| ||||| |   | | |   | ||| |||| ||| || || || || || ||||| ||  | || || || || | |||||||||||||||||||||||||||||||||||  || || ||||||||||
gtaggctttctttctcttagtattttctcttaggcatttggtggaataagaataaatgaattagcacccagaagttagcacatatgattcttccttctagggcttgctctattttatacaaatagttaaatttcatatcttgt-gcgattgattgagttaaattctgttgggtttgctagACTGGCCCTCCACAATATCGTAGCAGTACTATCTTTGAGGATGCTACTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGGCTTTAGATTGAAGTGGG
















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|298168977|gb|HO020281.1|HO020281
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|209719139|gb|BW674901.1|BW674901
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|209705241|gb|BW673781.1|BW673781
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|9819788|gb|BE555301.1|BE555301
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|5058455|gb|AI736866.1|AI736866
EST:     CCCGT-CTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: CC-GTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|209707871|gb|BW662077.1|BW662077
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|209716308|gb|BW684779.1|BW684779
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|9900212|gb|BE609180.1|BE609180
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCA
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCA
EST: gi|209725639|gb|BW663128.1|BW663128
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGG
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGG
EST: gi|213615049|gb|DB960774.1|DB960774
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|209727052|gb|BW680332.1|BW680332
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGA
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGA
EST: gi|26049090|gb|CA785543.1|CA785543
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|209700806|gb|BW683062.1|BW683062
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|213615212|gb|DB965020.1|DB965020
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|6134791|gb|AW133184.1|AW133184
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCT
EST: gi|209701094|gb|BW664196.1|BW664196
EST:     ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAG                         AGTGGACCGCCGCAGTACCGGAGCA
genomic: ACCGTTCTACCCCGACCATGACCTATCAAGCGTGGCGTAGGGATCCTGAGgtacgcctta ... tgcttgttagAGTGGACCGCCGCAGTACCGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcccttttgcagtttgttagaattgagtgagtgagggtgtatgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGAGTTCAGGTTGAAGTGGG
                    ttagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgccttacctttcattcttcccttttgcagtttgttagaattgagtgagtgagggtgtatgcttgttagAGTGGACCGCCGCAGTACCGGAGCAGAACGGTGTTCGAAGACGCGAGTCCTGAGTTGGTGAGGGATTTCTTTTGGGATGATGAGTTCAGGTTGAAGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG