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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaacgaaatccctaatttgttatattacactaaacaagattgaacaatatattttgatttgcttctgtatattgatagttaaatggtgtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGATTCCTCAATCAGAGAGCTTGCTCTGTCTCTGATAGTTGAAATGCTGAAAA

Basic information

species Glycine max
transcript GLYMA13G19230.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os04g42840.1 (Oryza sativa), 3'ss of exon 15
aaaaaacgaaatccctaatttgttatattacactaaacaagattgaacaatat--attttgatttgcttctgtatattgatagttaaatggtgtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGATTCCTCAATCAGAGAGCTTGCTCTGTCTCTGATAGTTGAAATGCTGAAAA
  |||      ||| |   |   ||||| |   |     ||||   | ||| |  | | |    |  | |  | || | | |||       |   |   ||||| |||||||| || || || | |||||||||||||||||||||||| ||||| || |  || ||| ||||||||||| |  | |  || ||||| || |
--aaattttcttccttgtatctctatatcaactttgggtagatctgaaaattttcaatctatactattgcattctaattacagtccttcaattatacaacagTATTTCAATCAAATCTTAACGGCTGTGCTTGAGGTGCTGGATGATTCTGATTCATCTACTAGGGAGATTGCTCTGTCTTTAGTTGCCGAGATGCTCAACA

upper sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G20190.1 (Arabidopsis thaliana), 3'ss of exon 15
aaaaaacgaaatccctaatttgttatattacactaaacaagattgaaca-atatattttgatttgcttctgtatattgatagtta--aatggtgtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGATTCCTCAATCAGAGAGCTTGCTCTGTCTCTGATAGTTGAAATGCTGAAAA
        || ||| |    ||  |||| |    | |   | || | ||  || ||||   | |   ||   ||  | ||   |   | |  | || |  |||||||||||||| |||||||| ||||| ||||| ||||| |||||   |||||  ||||||| |||||||||||| ||  ||||   ||||||||| || |
--ttggtaaactccgttgggtgggatat-atttcatagttgctttaccatgtacatttgcctatcaatcctaatggtcattcctcctacttttctactcccagTACTTCAATCAAATTTTGACGGTTGTTCTTGAAGTGCTCGATGACGAAGATTTTTCAATCAAAGAGCTTGCTCTTTCATTGATTTCTGAAATGCTAAAGA

upper sequence: GLYMA13G19230.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv07s0005g05030.t01 (Vitis vinifera), 3'ss of exon 12
aaaaaacgaaatccctaatttgttatattacactaaacaagattgaacaatatattttgatttgcttctgtatattgatagttaaatggtgtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGATTCCTCAATCAGAGAGCTTGCTCTGTCTCTGATAGTTGAAATGCTGAAAA
  |  | || ||   | |||   |  |  | |    |   |||    |||| | | || | ||  | || | || |||||| ||| |||| |   |||||||||||||||||||||||||||   | |||||| |  |||||||||| ||||| |||||| | || |||||||| ||  |||||||||||||||| ||||
ggaccatgatatttattattaagttaaaaaaatattatgtgatgtttcaatttttatttagtttttcctttttaatgatagctaagtggtatttatgcagTACTTCAATCAGATTTTGACAGCCATACTTGAGATTTTGGATGATTCTGATTCTTCAATCCGGGAACTTGCTCTTTCATTGATAGTTGAAATGCTAAAAA

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|18039838|gb|BM308132.1|BM308132
EST:     AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTG                         TACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
genomic: AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTGgtatttttaa ... gtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
EST: gi|21602116|gb|BQ612447.1|BQ612447
EST:     AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTG                         TACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
genomic: AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTGgtatttttaa ... gtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
EST: gi|13481639|gb|BG510982.1|BG510982
EST:     AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTG                         TACTTCAATCAGATTTTGACAGTTGT
genomic: AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTGgtatttttaa ... gtaattgcagTACTTCAATCAGATTTTGACAGTTGT
EST: gi|15337267|gb|BI497923.1|BI497923
EST:     AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTG                         TACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
genomic: AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTGgtatttttaa ... gtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
EST: gi|151394618|gb|EV264489.1|EV264489
EST:     AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTG                         TACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
genomic: AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTGgtatttttaa ... gtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
EST: gi|18735275|gb|BM528670.1|BM528670
EST:     AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTG                         TACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT
genomic: AACAGCTAGCTGAAGTGTCTATAGCCAATGATCATTCTGTTTGGACCCTGgtatttttaa ... gtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaatatattttgatttgcttctgtatattgatagttaaatggtgtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGATTCCTCAATCAGAGAGCTTGCTCTGTCTCTGATAGTTGAAATGCTGAAAA
                           tattgat  putative branch site (score: 3)
                         tatattgatagttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaacgaaatccctaatttgttatattacactaaacaagattgaacaatatattttgatttgcttctgtatattgatagttaaatggtgtaattgcagTACTTCAATCAGATTTTGACAGTTGTGCTTGAGGTGCTGGATGATTCAGATTCCTCAATCAGAGAGCTTGCTCTGTCTCTGATAGTTGAAATGCTGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
aaaaaac
- - - - - - - - - - - - - - - - ctaaaca