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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcatatatctgtaaaatacttaggttacaaaacaaatagagtcaactgctaagaagtcttactttttcctactcacctaagtttttaagctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAGAGGCTGATGCAAGAAGCATATCAGAGAGGTAGTGCTGACAATATCACAT

Basic information

species Glycine max
transcript GLYMA04G06250.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 8
-------------ctcatatatctgtaaaatacttaggttacaaaacaaatagagtcaactgctaagaagtcttactttttcctactcacc-taagtttttaagctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAGAGGCTGATGCAAGAAGCATATCAGAGAGGTAGTGCTGACAATATCACAT
               | ||| ||| ||   | |  |  ||  |    | || | |   | |   |   |  | | |    || | ||||     | |   | | | ||  |||||| ||||| || ||||| || |||||    ||  |||||||||||||||||||||||||||| ||||||||||||||||| ||||| || || || || |
gtttgttttctcgtccctatttcttta---tgcccat-ttgtatggtagatggtggatattcacacacaacccttcacagtcttcctcatagctaatacgtcaccatttatcagGAGGCTGTCGCAATGATCAAACCAATCCCAGACCCAGAGGAGGCAGCAAAGAGGCTGATGCAGGAAGCATATCAGAGAGGCAGTGCAGATAACATTACCT
















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|9984727|gb|BE658835.1|BE658835
EST:     GTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: GTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
EST: gi|192313213|gb|FK003333.1|FK003333
EST:     AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
EST: gi|120491569|gb|EH219736.1|EH219736
EST:     AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
EST: gi|254334939|gb|GR844724.1|GR844724
EST:     AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
EST: gi|6200840|gb|AW152940.1|AW152940
EST:     GTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: GTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
EST: gi|209722646|gb|BW654653.1|BW654653
EST:     AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
EST: gi|192313214|gb|FK003334.1|FK003334
EST:     AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
EST: gi|120492227|gb|EH220394.1|EH220394
EST:     AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
EST: gi|13311519|gb|BG405170.1|BG405170
EST:     AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAG                         GAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG
genomic: AGTTTCTTATTCTGGCCAGTGACGGGCTATGGGATGTTGTCTCTAATGAGgtttgtactg ... ctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgctaagaagtcttactttttcctactcacctaagtttttaagctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAGAGGCTGATGCAAGAAGCATATCAGAGAGGTAGTGCTGACAATATCACAT
                         tactcac  putative branch site (score: 1)
                                             ctttcttc  putative PPT
                                 taagtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcatatatctgtaaaatacttaggttacaaaacaaatagagtcaactgctaagaagtcttactttttcctactcacctaagtttttaagctttcttcagGAAGCTGTTGCTATGATAAAGCCAATTGAGGATGCAGAGGAGGCAGCAAAGAGGCTGATGCAAGAAGCATATCAGAGAGGTAGTGCTGACAATATCACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - -caactgc