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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtatcttcaaattttatttgctgacattttttctctgacagaacttttgcttatgtttttcacattaatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG

Basic information

species Glycine max
transcript GLYMA03G39500.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
---------------gtttggtatct--tcaaattttatttgctga--cattt-tttctctga--cagaacttttgcttatgtttttcacattaatatc-atagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
                | || | |||  |||  |  | |||  | |  |||||  || | | |  || || |  ||||| |   |   |  |   | ||  ||||| || ||  | |||||||||||  |||| ||||| || ||||||||  | ||||| || |||||||| ||||||| ||| ||||| |||||||| ||||
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctt-taactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 8
-----------------------------------------------gtttggt-atcttcaaattttatttgctgacattttttctctgacagaact---tttgcttatgtttttcacattaatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
                                                  || | |||||    |   | |     | ||  ||  |||| |||||||         | | ||||      |  ||   |||||||||||  | |||||||||||  |||| ||||||||||||||||| || || || || || || || |||||||  |||||||| || || || ||||
gtatgtctcctgaaatctgtgttggctacttgttccaaaaattgctgacctgattatctttctttaaaaataaaataaatccttgttctgccagaactaaaacaatctttattttatgtggtcttactctagATCCATTCAAGAAAAATGAATGTAAACCCTGATGTCAACTTTGAAGAGTTGGCACGATCTACGGACGACTTCAATGGTGCACAACTGAAGGCCGTTTGTG

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 7
----gtttggtatcttcaaattttatttgctgacattt---------tttctctgacagaacttttg------cttatgtttttcacattaatat--catagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
    || |       | |   |  | |||||||  |||         ||||      ||  | |||       || | || ||    |||  |      |||||||||||  |||||||||||||  | || |||||||||||||||||||| ||||| || || ||||| ||||| | |||||| || || || || ||||
gtcggtctcaacaacttatgctcaaattgctgaagtttgtcagtggctttcctcagtaggccatttatcacaactaacgtgttctgtattggtcctctgtagATCCATTCAAGGAAAATGAATGTAAATCCTGATGTCAACTTTGAAGAATTGGCTCGCTCAACTGATGACTTCAACGGAGCACAGCTAAAGGCAGTTTGTG

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
-------------------gtttggtatcttcaaatt--ttatttgctgacattttttctc----tgacagaacttttgc----ttatgtttttcacat-taatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
                   |||   | |  | || ||  | | |   |||  ||||| ||         ||  | ||| |    | |||||||    || |   |   |||||||||||  | |||||||| ||  | || ||||||||||| |||||||| ||||| || |||||||| ||||| | |||||| || || || |||||||
gtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 8
--------------gtttggtatcttcaaattttatttgctgacattttttctctgacagaacttttgctt---atgtttttcacattaatatcat--agATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
                | |    | || |||    || | |    |   | |      || |||   | ||   |  |    |  ||  || |  |  ||||||| ||  |||||||||||||  | || ||||||||||||||||| || || || || || |||||||||||||  || || || || ||||| || |
aataagaaagggattctagcccccctccaatccccttcggttttgtggctcccaaactagcactaaaggttccaaaataacgccgatctatgttgtgtagATCCACTCGAGGAAAATGAATGTGAATCCAGATGTCAACTTTGAAGAGTTGGCGCGTTCAACCGATGATTTCAATGGCGCTCAGCTAAAGGCTGTTTGCG

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 8
gtttggtatcttcaaattttatttgctg---------acatt--ttttctctgacagaacttttgcttatgtttttcacattaatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
|| ||   ||    ||| || | | ||          |||||  |      |  |||| || ||  | |  | |||||||||    |  |||||||| ||  | || |||| |||||| || |||||||| ||||||||| | ||||| |||||||||||||||||||  |||||||| |||||||| ||||
gtatgtcttcaatgaatattttcttctagatcattacacattgatcactctttgcagagctcttattgac-tctttcacattgtatttgtagATCCACTCGAGAAAGATGACTGTTCATCCGGATGTCAATTTTGAAGAACTGGCTCGATCCACAGATGATTTCAATGGGGCACAACTGAAAGCTGTTTGTG

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|9984894|gb|BE659002.1|BE659002
EST:     AAATTGAGTTCCCACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAG                         ATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTA
genomic: AAATTGAGTTCCCACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAGgtttggtatc ... aatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTA
EST: gi|7030457|gb|AW460240.1|AW460240
EST:     AAATTGAGTTCCCACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAG                         ATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTA
genomic: AAATTGAGTTCCCACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAGgtttggtatc ... aatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTA
EST: gi|209727654|gb|BW663794.1|BW663794
EST:     AAATTGAGTTCCTACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAG                         ATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTA
genomic: AAATTGAGTTCCCACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAGgtttggtatc ... aatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTA
EST: gi|209718166|gb|BW657812.1|BW657812
EST:     AAATTGAGTTCCTACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAG                         ATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTA
genomic: AAATTGAGTTCCCACACCCAACTGAAGAAGCAAGAGCCCGAATTCTACAGgtttggtatc ... aatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacattttttctctgacagaacttttgcttatgtttttcacattaatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG
                             ttatgtttttcacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggtatcttcaaattttatttgctgacattttttctctgacagaacttttgcttatgtttttcacattaatatcatagATCCATTCTCGGAAAATGAATGTTCACCCCGATGTCAACTTTGAAGAATTAGCTCGGTCCACAGATGATTTCAATGCAGCACAACTTAAAGCTGTCTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG