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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagatctttggctagatgttaggcatatgtgatttccatattatgtgctcttcatgcgtcatcttaatcatgataatctgcattatttttttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCCATTGTAACTCTCAATGGGAGGAATAT

Basic information

species Glycine max
transcript GLYMA13G17200.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 3
---------------aagatctttggctagatgttaggcatat--------gtgatttccatattatgtgctct--tcatgcgtcatcttaatcatgataatctgcattattt--tttta----------tttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCCATTGTAACTCTCAATGGGAGGAATAT
                 ||| |||   |  || | ||  ||||        | |  | |  | |   ||| |    ||   |   |   |  ||||||  |||| ||| ||||  |||||          | |||||||||| ||||||||||| ||||||| ||| ||||| || ||||||||  | ||| | || || ||||| | | | ||
gtttgctttcattacctgatttttctgtttatttcagttatatttttgaaagcgtatcctttgtggggtgattcagtctgacacaactattgtcatgaggatct-catgatttacttttaaacatatgtttctgcagTCATCTTATGGCTTTGTTGACTACTATGACCGCAGATCAGCTGCATTATCAATTTTGACACTTAATGGAAAGCAAAT

upper sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 3
aagatctttggctagatgttaggcatatgtgatttccatattatgtgctcttcatgcgtcatcttaatcatg-ataatctgcattatttttttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCCATTGTAACTCTCAATGGGAGGAATAT
 |   || | |  |   | |    |    |   | | || ||  ||||| ||    | || |   | | |    |   ||   ||  ||| | || |||||||||||||||| ||||| || |||||||| || || ||||||||  || | ||||| ||||| ||||| ||| || |
-attgctgttgtcatcagcttcctaagattttctccaattttccgtgctatttgctcatcttaccattgacatgtctcctcttttcctttctcatatgcagTCATCCTATGGTTTTGTCGATTACTTTGACCGGAGATCTGCTGCCCTTTCTATTGTGACTCTGAATGGAAGGCATCT
















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|208327271|gb|GE122409.1|GE122409
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
EST: gi|208232849|gb|GE030376.1|GE030376
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCG
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCG
EST: gi|193545482|gb|FK503989.1|FK503989
EST:     CCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGACCGCAGTTCTGCTGCATTTGCC
genomic: CCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
EST: gi|13252197|gb|BG363100.1|BG363100
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
EST: gi|193328920|gb|FK295164.1|FK295164
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGC
EST: gi|208052196|gb|GD853481.1|GD853481
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
EST: gi|13789938|gb|BG652529.1|BG652529
EST:     TTTCAACTGCTGGCGCCCTTGAAGGAT-TAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
EST: gi|19348273|gb|BM892805.1|BM892805
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
EST: gi|193355897|gb|FK319124.1|FK319124
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
EST: gi|42723064|gb|CK768963.1|CK768963
EST:     TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAG                         TCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC
genomic: TTTCAACTGCAGGCGCCCTTGAAGGATGTAAACTTATTAGGAAAGAGAAGgtcagctttg ... ttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcttcatgcgtcatcttaatcatgataatctgcattatttttttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCCATTGTAACTCTCAATGGGAGGAATAT
                tcttaat  putative branch site (score: 3)
                                     ttatttttttattt  putative PPT
                        atgataatctgcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagatctttggctagatgttaggcatatgtgatttccatattatgtgctcttcatgcgtcatcttaatcatgataatctgcattatttttttatttgcagTCATCCTATGGCTTTGTGGACTACTTTGATCGCAGTTCTGCTGCATTTGCCATTGTAACTCTCAATGGGAGGAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA