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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgtatctaattttgaatgtgcttaattatgttttatgttctttttctttgtttgaagtgttttttttcctctactgttaatattctgctgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCATTGATGAAGTAGACAGTTTTTTGGGTCAGCGTCGTGGAACAGATCACGA

Basic information

species Glycine max
transcript GLYMA06G13800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13800.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0098g01260.t01 (Vitis vinifera), 3'ss of exon 2
----tttgtatctaattttgaatgtgcttaattatgttttatgttctttttctttgtttgaagtgttttttttcctctactgttaatattctgctg-ctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCATTGATGAAGTAGACAGTTTTTTGGGTCAGCGTCGTGGAACAGATCACGA
    |    || |  || | ||  || ||||||  || || |    |||  |  |       || | | |||      |  ||| || || |     ||||||||| ||||||||||||||||||||||| || || || ||||| || || ||||||||||| || || | ||||||||||||||| ||   |||||| || ||
ttgttgaaaatttggttgtaaagttgtttaattg-gtcttgt----tttaccactaccaagtgtttctctttgatctgaacgttgatcttttctaaactctgcagTGGCTGCTGTATTTAGCTTGGCTTACAAACTCCAACCTGCTATTATCTTCATTGATGAGGTTGATACTTTTTTGGGTCAGCGCCGGACAACAGACCATGA

upper sequence: GLYMA06G13800.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13213 (Selaginella moellendorffii), 3'ss of exon 2
tttgtatctaattttgaatgtgcttaattatgttttatgttctttttctttgtttgaagtgttttttttcctcta-ctgttaatattctgctgctctg--cagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCATTGATGAAGTAGACAGTTTTTTGGGTCAGCGTCGTGGAACAGATCACGA
                                                   || ||   || | |||      || ||| |   |||    | ||  |  ||||  |||||||||||| ||||||| | ||||| |||||| | ||||| ||||| |||||||| ||||| || ||||| |  ||  | |  ||   ||||||
---------------------------------------------------gtatgttttgctctttcattggtagctgatcgaatttcttttcttcgtacagTGACTGCTGTATTTACCTTGGCTCACAAGCTCCAGCCTTCTATCATCTTCATCGATGAAGTGGACAGCTTCTTGGGACGTCGAGGAGTTACCAGTCACGA
















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|193424886|gb|FK386059.1|FK386059
EST:     GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTG                         TTGCTGCTGTATTTAAGCTTGGCTTAT
genomic: GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTA-GCTTGGCTTAT
EST: gi|254332455|gb|GR843932.1|GR843932
EST:     GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTG                         TTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
genomic: GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
EST: gi|5606071|gb|AI900169.1|AI900169
EST:     AGAATATCANACCTGATNGAGCA-GTGGTTTTGGGATGCCCAAAAGCTTG                         TTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
genomic: AGAATATCAAACCTGAT-GAGCAAGTGGTTTGGGGATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
EST: gi|193348000|gb|FK311812.1|FK311812
EST:     GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTG                         TTGCTGCTGTATTTAGCTTGGCTTAT
genomic: GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTAGCTTGGCTTAT
EST: gi|151412804|gb|EV282616.1|EV282616
EST:     GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTG                         TTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
genomic: GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
EST: gi|192324866|gb|FK015362.1|FK015362
EST:     AGAATATCAAACCTGATGAGCAAGTGGTTTGGGGGATGCCCAAAAGCTTG                         TTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
genomic: AGAATATCAAACCTGATGAGCAAGTGGTTTGGGG-ATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
EST: gi|11687417|gb|BF595093.1|BF595093
EST:     GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTG                         TTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
genomic: GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
EST: gi|7638877|gb|AW733269.1|AW733269
EST:     GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTAG                         TTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
genomic: GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCA
EST: gi|208318942|gb|GE112011.1|GE112011
EST:     GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTG                         TTGCTGCTGTATTTAG
genomic: GAGAATATCAAACCTGATGAGCAAGTGGTTTGGGGATGCCCAAAAGCTTGgtaagtgcac ... tgctctgcagTTGCTGCTGTATTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttgtttgaagtgttttttttcctctactgttaatattctgctgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCATTGATGAAGTAGACAGTTTTTTGGGTCAGCGTCGTGGAACAGATCACGA
                               tgttaat  putative branch site (score: 3)
                                       ttctgct  CT-rich tract
              tgtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgtatctaattttgaatgtgcttaattatgttttatgttctttttctttgtttgaagtgttttttttcctctactgttaatattctgctgctctgcagTTGCTGCTGTATTTAGCTTGGCTTATAAGCTTCAGCCTGCCATCATATTCATTGATGAAGTAGACAGTTTTTTGGGTCAGCGTCGTGGAACAGATCACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - -gaatgtg
- - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attctgc