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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagcagaatttttctgaagcctgttatatgtatgaatttatgtattttttttaatacctggtagactctaataaacaatacccttggcatttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT

Basic information

species Glycine max
transcript GLYMA13G42800.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 8
--------------------gaagcagaatttttctgaagcctgttatatgtatgaatttatgtattttttttaatacctggtagactctaataaa-caatacccttggcatttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT
                     |   | | | |   || ||  | | |  || || | |     | |   || |  ||   | |    | || ||   | |||||  | |  ||   || || |||||| | || || || ||||| || |||||||||||||| |||||||| ||||| || |||||||||||||||  ||||||||| ||  | || || 
gtgagcttttatttcacactaacatatactctacttggagaatatcaagtgaat-actgcccttctcaattatcctataagtttcgttgtactatttctatacctgttgtcttct-tgtagCTTTGAGCAGCATGAGGCCCCAGGTTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTC

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 8
----------------------------------------gaagcagaatttttctgaagcctgttatatgtat---gaatttatgtattttttttaatacctggtagactctaataaacaatacccttggcatttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT
                                          || | | | |   || ||  | ||   || ||   ||  ||||  ||| |  | ||    |  | |  | |  || ||  |   | || | | |  || || |||||| | || || || ||||| || |||||||||||||| |||||||| || || || ||||||||||| |||  ||||||||| ||  |  | || 
gtgagcttttagtttacactttttatttcctacaatatgttcagtatactctacttggagaatattgggtggatactgaccttatcaattatcctaaaagtttccttgtatttt-tatacc-tgttcatgtcttct--tgtagCTTTGAGCAGCATGAGGCCCCAGGCTCAAGATCATTTTTCACTGAGATTATAGCCTCAATTTCGGACATAAAGTTTTCGAAGGATGGGAGGCATCTTCTC

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
---------------------------------------------------------------------------------------gaagcagaatttttctgaagcctgttatatgtatgaatttatgtattttttttaatacctggtagactctaataaacaat-acccttggcatttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT
                                                                                        |     |||||||||      | || |  | |   | ||    ||     ||||||      ||  ||| |  |   |  |   |||     |    ||||||||| |||| |||||| || || || |||||||||||||| ||||| ||||| || || || || || |||||    |||||||| ||||||||||||
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctct--tttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT

upper sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
gaagcagaatttttctg--aagcctgttatatgtatgaatttatgtattttttttaatacctggtagactctaataaacaataccct--tggcatttg-atgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT
      | |||  || |  ||       | |   || | |||     |     ||  ||  | ||   || |  |  |  |  |  |  | | | ||| |||||| ||||||||||| || || || || || |||||||||||||| ||||| ||||| || || || ||||| ||||||   |||||||| ||||  ||||| 
-----tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttagtgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC

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|7686354|gb|AW757002.1|AW757002
EST:     CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACTgtaagtacat ... tttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
EST: gi|19936402|gb|BQ080848.1|BQ080848
EST:     CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACTgtaagtacat ... tttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
EST: gi|18730643|gb|BM525996.1|BM525996
EST:     CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACTgtaagtacat ... tttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
EST: gi|5770902|gb|AI974076.1|AI974076
EST:     CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACTgtaagtacat ... tttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
EST: gi|193711274|gb|FK646095.1|FK646095
EST:     GTCTTGTTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
genomic: GTCTTG-TTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACTgtaagtacat ... tttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
EST: gi|21887329|gb|BQ740542.1|BQ740542
EST:     CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT
genomic: CGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACTgtaagtacat ... tttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttaatacctggtagactctaataaacaatacccttggcatttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT
                      tctaataaacaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagcagaatttttctgaagcctgttatatgtatgaatttatgtattttttttaatacctggtagactctaataaacaatacccttggcatttgatgcagATTTGAGGAACAGGAAGCTCCAGGGTCCAGATCATTTTTCACGGAGATTATTGCTTCTATCTCGGACATAAAATTTGGGAAGGATGGTAGATACATACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - agcctgt
- - - - - - - - - - - - - - -tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - atacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acccttg