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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactgctattcaggcattttgctatggcaaacccattgtaggctttttttttcatagtatgatgcaaatacggcaaggttctaattttcaatctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGATGAAGAGGTCATTCGGTTTCAAATAGGAGAGGTTTTTGCTCATGTGCCAA

Basic information

species Glycine max
transcript GLYMA20G36840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0081g00080.t01 (Vitis vinifera), 3'ss of exon 2
---cactgctattcaggcattttgctatggcaaacccattgtaggctttttttttcatagtatgatgcaaatacggcaaggttctaattttcaatctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGATGAAGAGGTCATTCGGTTTCAAATAGGAGAGGTTTTTGCTCATGTGCCAA
   ||   || |||   |  |||   |  ||||    |   | ||    | | |  ||  |  | ||| |   |        | ||||     || | | ||||||||||| || ||| |||||||||||||||| ||||||||||||||||| || ||| |  | || || || |||||||||||||||||||||||||| |
ttccatgcctgttccatctctttataa--gcaattaaaacatcggtcaatctgtatatgtttagttgccatccccttttaact-taatggcttatttcttcagGAAACAAATGAAAATCTGGAGGATGCAAGCAATGAGTTGATTCTCACAGACGAGGAGATGGTCCGCTTCCAGATAGGAGAGGTTTTTGCTCATGTGCCGA
















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|209727380|gb|BW651928.1|BW651928
EST:     GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAG                         GAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
genomic: GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
EST: gi|31473825|gb|CD415853.1|CD415853
EST:     GGTTGAACAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAG                         GAAACCAACGATAATTTGGAGGATGCACAGCAACGAGTTGATTCTCACAGA
genomic: GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCA-AGCAACGAGTTGATTCTCACAGA
EST: gi|192296333|gb|FG989786.1|FG989786
EST:     GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAG                         GAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
genomic: GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
EST: gi|254319229|gb|GR830577.1|GR830577
EST:     GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAG                         GAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
genomic: GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
EST: gi|192297215|gb|FG990591.1|FG990591
EST:     TGAGATCAAAATCGCTAAG                         GAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
genomic: TGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
EST: gi|209727379|gb|BW651927.1|BW651927
EST:     GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAG                         GAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
genomic: GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
EST: gi|254319228|gb|GR830576.1|GR830576
EST:     GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAG                         GAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
genomic: GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
EST: gi|151396125|gb|EV266002.1|EV266002
EST:     GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAG                         GAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
genomic: GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
EST: gi|298174302|gb|HO017638.1|HO017638
EST:     GGTTGAACAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAG                         GAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT
genomic: GGTTGAATAATCGCTTTCACGAGCTTGAGGATGAGATCAAAATCGCTAAGgtaatctatt ... atctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttcatagtatgatgcaaatacggcaaggttctaattttcaatctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGATGAAGAGGTCATTCGGTTTCAAATAGGAGAGGTTTTTGCTCATGTGCCAA
                                 ttctaat  putative branch site (score: 2)
                                              tctttac  putative PPT
                                    taattttcaatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactgctattcaggcattttgctatggcaaacccattgtaggctttttttttcatagtatgatgcaaatacggcaaggttctaattttcaatctttacagGAAACAAACGATAATTTGGAGGATGCAAGCAACGAGTTGATTCTCACAGATGAAGAGGTCATTCGGTTTCAAATAGGAGAGGTTTTTGCTCATGTGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
cactgct
- - - - -tcaggca
- - - - - - - - - -tgctatg
- - - - - - - - - - - - - -caaaccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgca