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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacacatgttttttctttccttttttggattctcggttgatagtagtttttttctgtgtttttccttttagtgtacttacattacttatttgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCTTTGATGCAGCTGCCAATGGCCCTGTTAGTCGAAGTGGTTCATCAAGATC

Basic information

species Glycine max
transcript GLYMA12G37100.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 21
gacacatgttttttctttccttttttggattctcggttg-atagtagttttt-----ttctgtgtttttccttttagtgtacttacattacttatttgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACC---TGGTGATGACTGGAGATCTGCCTTTGATGCAGCTGCCAATGGCCCTGTTAGTCGAAG---TGGTTCATCAAGATC
        |||  | |||| ||||    | ||||  ||  |  || ||   |       |  | |||    || |     | ||   ||  ||| ||  |||||||| || ||||||| || |||  |   | |   |||||||||||||||||| || |||||||| || |||||||| ||||||      |    || ||  ||      
----gtcttttcctttttcattttacaaactctccatttcactgtggtccatggaatccccctatttgaaattctgaaaaatttggttt--ttacttcatttgcagAAAGCAGCCCAAAAACCAGTGGTCCATCCGGTGGTGATGACTGGAGATCAGCATTTGATGCTGCAGCCAATGGACCTGTTGACTACAACTCTGATTTGTC------
















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|14011037|gb|BG725959.1|BG725959
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|58018015|gb|CX704757.1|CX704757
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|18038693|gb|BM306987.1|BM306987
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|209705823|gb|BW675928.1|BW675928
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|151401960|gb|EV271773.1|EV271773
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|58021278|gb|CX708020.1|CX708020
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|51336285|gb|CO980151.1|CO980151
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|37995741|gb|CF807330.1|CF807330
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|58024379|gb|CX711120.1|CX711120
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
EST: gi|254322389|gb|GR837803.1|GR837803
EST:     TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAG                         AGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT
genomic: TCATGACAACCGAGCAGCTGCTGCCTCTGGCTGGTCAAATGGTAGTGCAGgtatgtgtaa ... tgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttttctgtgtttttccttttagtgtacttacattacttatttgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCTTTGATGCAGCTGCCAATGGCCCTGTTAGTCGAAGTGGTTCATCAAGATC
                            tacttac  putative branch site (score: 1)
                                           tttgtttt  putative PPT
                                   attacttatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacacatgttttttctttccttttttggattctcggttgatagtagtttttttctgtgtttttccttttagtgtacttacattacttatttgttttgcagAGAGTAGCCCAAGAAGCAGCAGCGGACCTGGTGATGACTGGAGATCTGCCTTTGATGCAGCTGCCAATGGCCCTGTTAGTCGAAGTGGTTCATCAAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- cacatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtgtac