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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattttgaattgtaatacagttcttttgttttaactttttcagccttcagctaattagcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT

Basic information

species Glycine max
transcript GLYMA13G00610.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g45110.1 (Oryza sativa), 3'ss of exon 8
gtgagattttgaattgtaatacagttcttttgt-tttaactttttcag----ccttcagctaattagcttatgtctcgaat----ttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
|| ||  ||| | ||  |||| | |    |    ||| | | |||  |          ||||| ||  |    | | | ||    | ||||||| ||||||||||| ||||| ||||||||| | || |||||||| ||||||||| |||||||||| || |  || || || |||   ||||| || |
gtcagtattt-atttacaatatattgaagtgacatttgattcttttgggggcttacttgctaaatacatatcattttgcatatcttcagATGGTAGATCCTGGTGGAATTGCTAATTGGTCAGTTACACATGTTGATTGGTCTGAGGGAAAATGGCATCCGAGGTCATATAGAGCTGCAGATGTCACCT

upper sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g48700.1 (Oryza sativa), 3'ss of exon 8
gtgagattttgaattgtaatacagttcttttgttttaactttttcagccttcagctaatt---agcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
|| |||  |   |         |  |  | | ||| |  | | |   | | |   | |||    ||   | |      |  |||||||||||||   ||| ||||||||||||||| | || |||||||| ||||||||  |||||||||| || ||| |||||||||||   ||    |  |
gtaagaactctcaaaaactcttaaatgatgtttttcagttgtgtttacttcccagtgatttcaggccgttattgtacctgcagATGGTTGATCCAACTGGAATTGCAAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCTAAAGCTTACAGGGCTGTTGACACAAGCT

upper sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
--------gtgagattttgaattgtaatacagttcttttgttttaactttttcagccttcagctaattagcttatg-tctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
         | | |||||||||||  ||  || | | ||   ||      ||  || ||    | ||  ||||    | ||   || ||||||| ||||||||||| ||  | ||||||||| | || |||||||| ||||||||  |||||||||| ||||  || || || |||   |||||||| |
gtcagtaaataatattttgaattgatatttagctttctt--cttggtccctt--gcttttctttcatatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT

upper sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G138505_T01 (Zea mays), 3'ss of exon 8
----gtgag-attttgaatt--gtaatacagttcttttgttttaacttttt--cagccttcagctaattagcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
    || |  ||||| || |  || ||  |  | ||||   |  ||   ||     ||||    || |    || ||| |    ||||||||||||| |||||||| || || || |||||| | ||||||||||| ||||| ||| |||||||||| ||||  || || || |||   |||||||| |
gttagtaattatttttaactctgttatttaccttttttccctcgaccccttgcttccctttttttagtacagttgtgtttattctttagATGGTTGACCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACAT

upper sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
----gtgaga-ttttgaattgtaatacagttct--tttgttttaactttttcagccttcagctaattagcttatgtctcgaattt-agATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
    || |   |||| || ||| ||     | |  |||  |  | |  || |   |||     | |    |||||| | ||  || ||||||| ||||||||||| || || || |||||| | ||||||||||| ||||| ||| |||||||||| ||||  || || || |||   |||||||| |
gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT

upper sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G040920_T02 (Zea mays), 3'ss of exon 9
-----------gtgagattttgaattgtaata--cagt---tcttttgtttta-actttttcagcctt-------cagctaattagcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
            |||  |||  | ||| |  |   | |   || | ||| | |  ||||| ||||| |       | || |||| || ||| | |   |  |||||| | || || | ||| ||||| ||||||||  |||| |||||||||||||||||  | || |||||||| ||| ||||||||||  ||||||| ||||
gtcagtacacaatgacctttc-agttgcaggaattaatttgtcatctgtctaatgcttttacagccctgttgacactgcaaatttgcatatctgtatcaactagATGATGGACCCAGATGGAATTGCTAATTGGTCTGTAACCCATGTTGACTGGTCTGAAGGGAAGTGGCACCCGAAAGCTTACAGGGCAAAGGATGTCACTT

upper sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
lower sequence: AT4G30060.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgagattttgaattgtaatacagttcttttgttttaactttttcagccttcagctaattagcttatgtctcgaatt-tagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
|| | |     | ||  ||  ||       | |   |   | | ||   || | ||   |    ||| | |    ||  ||||| ||||||| ||||||||||| || ||| |  |||| || ||||| |||||||||||||| ||||| || ||| | || | | || ||||| | ||  
gtaataaacc-attttcaactcaaaaagactataaaactctctgcattttttatcttcatgttatatatttttggttgcagATGCTTGATCCCGGTGGCATTGCTAACTGGACTGTAACACAAGTTGATTGGTCTGAGAGAAAGTGGCATCCCAAAACATATATGCCTGAGGATATCACAC

upper sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv11s0103g00490.t01 (Vitis vinifera), 3'ss of exon 8
-------------gtgagattttgaattgtaatacagttctt----ttgttttaactttttcagccttcagctaattagcttatgtctcgaattt---agATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
                |  | ||   | ||| || |  | ||     || | ||   |  |||  |   |   |||  | || | ||    ||||   ||||  ||||||| |||||||||||||| |||||| | || |||||||||||||||||   ||| ||||| |||||||| ||||||||||||||||||| ||
gtgagatatatataccatttgttccttggtattatatcttttggctctgctctagtctcatcattcccaactgaatatggttctttcatctatttgtcagATAATTGATCCAGGTGGCATTGCAAACTGGTCAGTTACACATGTTGACTGGTCTGAAGCAAAGTGGCATCCAAAATCATACAGGGCTCAGGATGTTAATT

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|254349102|gb|GR860374.1|GR860374
EST:     AGGGGAAGAA-TGCA-TGCTGATGAACATTACTTGCCGA-CATC-TCCAG                         ATGGGTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGG
genomic: AGGGGAAGAATTGCATTGCTGATGAACATTACTTGCCGACCTTCTTCCAGgtgagatttt ... tcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGG
EST: gi|120492868|gb|EH221035.1|EH221035
EST:     AGGGGAAGAATTGCATTGCTGATGAACATTACTTGCCGACCTTCTTCCAG                         ATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGG
genomic: AGGGGAAGAATTGCATTGCTGATGAACATTACTTGCCGACCTTCTTCCAGgtgagatttt ... tcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGG
EST: gi|15662506|gb|BI699877.1|BI699877
EST:     GAACATTACTTGCCGACCTTCTTCCAG                         ATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGG
genomic: GAACATTACTTGCCGACCTTCTTCCAGgtgagatttt ... tcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGG
EST: gi|15812840|gb|BI785115.1|BI785115
EST:     AGGGGAAGAATTGCATTGCTGATGAACATTACTTTTCTACCTTCTTCCAG                         ATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGG
genomic: AGGGGAAGAATTGCATTGCTGATGAACATTACTTGCCGACCTTCTTCCAGgtgagatttt ... tcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttgttttaactttttcagccttcagctaattagcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT
     tgttttaacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagattttgaattgtaatacagttcttttgttttaactttttcagccttcagctaattagcttatgtctcgaatttagATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG