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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtctttactttttcttttacattttgtggttcctttttattatccagaaatctaatactgattgtactgatatggctgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA

Basic information

species Glycine max
transcript GLYMA16G06850.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G27300.1 (Arabidopsis thaliana), 3'ss of exon 5
ttgtctttactttttcttttacattttgtggttcctttttattatccagaaatctaatactgattgtactgatatggctgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA
       |   ||| || ||| |||||||       |   |||||  ||| |   |||| |  | ||| | |  |   || |  ||  |  | ||   |||||||||||||||||||||  |  |||||||||||||||| ||||| |||||| | |||||||||||| | || ||| || ||||||||   ||||||||
------gtgagtttactgttagattttgt-------taacattatt-agatagagaatatt--tggtaataacttcattggaaatgtatattgtttccagCTGATCTTGGTGGATGGACTAGGATTGTTGTTGAGAAACCATTTGGAAAGGATTTGGAATCTGCAGAGCAGCTGAGTTCTCAGATTGGAGCCTTGTTTGA

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------------------------ttgtctttactttttcttttacattttgtggttcctttttattatccagaaatctaatactgattgtactgatatgg-ctgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA
                                                                      ||   | |||   ||  | | ||||||     |    ||    || ||    |   |  ||  |     | || |   ||  ||   ||     ||   ||||||||||||||||||||||||  ||||||| ||||| || ||||| ||||| || |||||||||||| |||| ||| || |||||||| |||| |||||
gtgagtccctttcagctgtggaatttattacttggataaaatgttaacctgcttgagcctaggacacgtatttcatctacgagttagtcttcattttagtagttagcttagaaatacaagttttagacgctt-tgaagttcatgtaaactatattgtctcataatttccagCTGATCTTGGTGGATGGACACGGATTGTTGTGGAGAAGCCATTTGGCAAGGACCTTGAATCTGCAGAGCAACTGAGTTCTCAGATTGGAGAGTTATTTGA

upper sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 5
ttgtctttactttttcttttacattttgtggttcctttttatt---atccagaaatc-taatactgattgtactgatatggctgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA
 |    || |   |||   || ||  ||  |        ||||    | |||||    |||  ||   | |      ||| ||  || || |    |||   |||| |||||||||||||||||||  |||| |||||||| ||||| || |||||| | || ||||||||| |||| ||| |  |||||||| |||| |||||
-taagattcccagttcaagtagatgctgaagcctaccagtatttaggttcagaacctgtaaatctagatctttatgaatgccttgatgtgatc---ttttccagCTAATCTTGGTGGATGGACACGCATTGTGGTTGAGAAGCCTTTCGGCAAGGATTTGGATTCTGCAGAGCAACTTAGTGCCCAGATTGGAGAGTTATTTGA

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|21637841|gb|BM107996.1|BM107996
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACACCTGTTGTTTGTTGAAAAACCTTTTTGGTAA
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTT-GTTGAGAAACCTTTT-GGTAA
EST: gi|16278453|gb|BI942912.1|BI942912
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACACGCGTTGTTGTTGAGAAAACCTTTTGGTAAG
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAG-AAACCTTTTGGTAAG
EST: gi|192310375|gb|FK002255.1|FK002255
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGG
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGG
EST: gi|11273943|gb|BF324331.1|BF324331
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTGGTTGCATGAATAAAT                         CTGATCTTGGTG-ATGGACACGTGGTGGTGT-GAGAAACCTTTTGG
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGG
EST: gi|16348194|gb|BI973789.1|BI973789
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGG
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGG
EST: gi|254331186|gb|GR843305.1|GR843305
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGG
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGG
EST: gi|9986040|gb|BE660148.1|BE660148
EST:     GTATATCCATCAAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACAC
genomic: GTATATCCATCA-GTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACAC
EST: gi|16348742|gb|BI974337.1|BI974337
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGG
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGG
EST: gi|37995559|gb|CF807148.1|CF807148
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACACGTGTTGTTGTT
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTT
EST: gi|15663680|gb|BI701051.1|BI701051
EST:     AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAAT                         CTGATCTTGGTGGATGGACACGTGTTGGTGTTGA
genomic: AGTATATCCATCAGTTTGCAAGATGATCAAGACTTGTTGCATGAATAAATgtaagatgct ... cttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagaaatctaatactgattgtactgatatggctgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA
                     tactgat  putative branch site (score: 2)
                                ctgcatctgcttcctt  putative PPT
     aatctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtctttactttttcttttacattttgtggttcctttttattatccagaaatctaatactgattgtactgatatggctgcatctgcttccttttcttagCTGATCTTGGTGGATGGACACGTGTTGTTGTTGAGAAACCTTTTGGTAAGGATCTAGAATCTGCAGAGGAACTCAGTACTGAGATTGGAAAGTTGTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA