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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgagacttcattgtaattttttttcttaaaaagttatccactgtattcatgtttttatttgtgattacattgcacttgttttggtatcctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG

Basic information

species Glycine max
transcript GLYMA13G16040.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
gttgagacttcattgtaattttt-tttcttaaaaagttatccac-tgtattcatgtttttatttgtgattac-attgcacttgttttg--gtatcctatgat-----agAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG
            || |||||||    |  ||  ||| ||  ||  |  ||   |||   |  || |  | ||   ||  | ||   ||  ||||| | ||||     |||| |||||||||||||| |||||||| ||||| ||||||||||| ||||||||||   | || ||||| || ||| | | ||| |||
-------gcaagttataattttaacatgctaggaagctaggcatgtccatatgtgtacctccttttcttgaccgctgttcatgccatgatgtatcttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG

upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
gttgagacttcattgtaattttttttcttaaaaagtt---atccactgtattcatgtttttatttgtgattacattgcacttgttttggtatcctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG
              | || |  |||  | | || | |   || ||     |   |  ||   |||||   |||||    |||   ||  |||  ||    || | |||||||| |||||||||||||| ||||| |||||||||||||| ||||| |   |  | ||| | || ||  |   ||| |||
--------------gcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacatgatgctttgctttttattatac---agCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG

upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G014805_T02 (Zea mays), 3'ss of exon 11
gttgagacttcattgtaattttttttcttaaaaagttatccactgtattcatgtttttatttgtgattacattgcacttgttttggtatcctatgat--agAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG
              | |  |  ||| ||||  |   |    | || || | |  | | |||    |      | ||      || |  |  ||| ||  |||| |||||||| |||||||||||||| ||||| |||||||||||||| || || |   |  | ||||| || ||  | | ||| |||
--------------gcatgtgatttccttatcatact--taaatgcataccttctctcattcactacattcatacatgatgctttgctttttattatacagAGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACCGATACAACATCGAAAAGGTCTTACACAGCCAATCAG

upper sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 30
gttgagacttcattgtaattttttttcttaaaaagttatccactgtattcatgtttttatttgtgattacattgcacttgttttggtatcctat----gatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG
        |    |||  ||| | |   | |||   |||      | | | | | ||||||| |  |||  ||  | || |||    || |  |     | ||||||||||||||||||||||||||||||| ||||||||  | |||||| |||||| ||||||||||||  | ||||| |  || |||
-------gtgtggtgtg-tttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttat-ttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG

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|58015534|gb|CX702276.1|CX702276
EST:     GCCGTCNTGAGTACCTTCAAGATTCTGACGTTGTATCCAGTCGTTTTCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACT
genomic: GCCGTCCTGAGTACCTTCAAGATTCTGACGTTGTATCCAGTCGTTTTCAGgttgagactt ... cctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACT
EST: gi|58015738|gb|CX702480.1|CX702480
EST:     GCCGTCCTGAGTACCTTCAAGATTCTGACGTTGTATCCAGTCGTTTTCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACT
genomic: GCCGTCCTGAGTACCTTCAAGATTCTGACGTTGTATCCAGTCGTTTTCAGgttgagactt ... cctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACT
EST: gi|209699336|gb|BW664055.1|BW664055
EST:     AAGATTCTGACGTTGTATCCAGTCGTTTNCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACT
genomic: AAGATTCTGACGTTGTATCCAGTCGTTTTCAGgttgagactt ... cctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACT
EST: gi|57573985|gb|CX546960.1|CX546960
EST:     GCCGTCCTGAGTACCTTCAAGATTCTGACGTTGTATCCAGTCGTTTTCAG                         AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACT
genomic: GCCGTCCTGAGTACCTTCAAGATTCTGACGTTGTATCCAGTCGTTTTCAGgttgagactt ... cctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattcatgtttttatttgtgattacattgcacttgttttggtatcctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG
         tttttatttgtgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgagacttcattgtaattttttttcttaaaaagttatccactgtattcatgtttttatttgtgattacattgcacttgttttggtatcctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG