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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgttcatgaggaattccttttctcactcaggttttttatgattatcttttgtctcatgttttaatatctgtgtccag

Basic information

species Glycine max
transcript GLYMA16G03170.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 4
ATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtacttt---gttcatgaggaattccttttctcactcaggttttttatgattatcttttgtctca-tgttttaatatctgtgtccag---
 ||||||| || ||  | || |||||| |||||||||| |||||| | | ||||||||||||||| ||||| ||||| || || || || |||||||||||||  ||   ||     | ||||     || ||  |  | |  |       ||| |||||| |   |   |   |  |    ||      
GTATCTGCAAGTATCACGGGTGATATTATTCTTGCTGCTGCATATTCCCGTGAGCTGCCACGATACGGTCTAGAAGTTGGTCTGACCAACTATGCTGCAGgtatatttatgtctgcaaagaatgtaaattgtctatt-gttactaagcacatatattttgtattgctaactccttgcccacatcttctag

upper sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 4
----ATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgttcatgagga-attccttttctcactcag-gttttttatgattatcttttgtctcatgttttaatatctgtgtc-cag
    ||||||||||| || || || ||||| ||||||||| | || ||  | |||||| |||||||||||||||||||||| || || || || ||||| || |||| ||| | ||||   | | |   |   |  |  |   | |||||   |  |  | | |    |   | || | |  | |   ||
AATCATATCTGCTAGTATAGCGGGTGATATGGTTCTTGCTTCTGCCTACTCGCATGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAgctggtattttttccatggaaataatgtataaattgcatattatattttaatgtatttatatattctctaaatcaacacccatcttgtag

upper sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G163081_T03 (Zea mays), 5'ss of exon 4
ATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgttcatgagga-attccttttctcactcag-gttttttatgattatcttttgtctcatgttttaatatctgtgtc-cag
||||||||||| || || || ||||| ||||||||| | || ||  | |||||| |||||||||||||||||||||| || || || || ||||| || |||| ||| | ||||   | | |   |   |  |  |   | |||||   |  |  | | |    |   | || | |  | |   ||
ATATCTGCTAGTATAGCGGGTGATATGGTTCTTGCTTCTGCCTACTCGCATGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtattttttccatggaaataatgtataaattgcatattatattttaatgtatttatatattctctaaatcaacacccatcttgtag

upper sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM5G815894_T03 (Zea mays), 5'ss of exon 4
ATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgttcatgaggaattcctttt----ctcactcaggttttttatgattatcttttgtctcatgttttaatatctgtgtccag-------
|| |||||||| || || || ||||| ||||||||| | || ||  | |||||| |||||||||||||||||||||| || || || || ||||| || |||| |||        | |||    | |      ||    |    || |||| | | | |  || |  |||  | |   |     ||        
ATCTCTGCTAGTATAGCAGGTGATATGGTTCTTGCTTCTGCTTACTCGCATGAGTTGCCACGATATGGTCTTGAAGTTGGTCTGACCAACTATGCAGCTGgtaatttcccttctggaaatattgtgtaaattgcatattgtaccttaatgaatttatatattcactagttcaactgcttacactcatcttgtag

upper sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 5'ss of exon 4
ATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgttcatgaggaattccttttctcactcaggttttttatgattatcttttgtctcatgttttaatatctgtgtccag----------------------------------------------------------------
| ||| |||||||||||||| ||||| || |||||| | |||||| | |||||||| || |  ||||| |||||||| || || || || |||||||||||||   | || || || ||||  ||   |    |   || ||||  ||| | |  ||| | |||  ||  ||  |||| |                                                                   
ACATCCGCTAGCATTGCTGGTGATATAGTCCTTGCTTCTGCATATTCTCATGAGCTACCTCACTATGGACTTGAAGTTGGTCTGACCAACTATGCTGCAGgta---tatttatcagaaattggttcattgttcctatttatttaaaatt-tgtcatgttt-atgaatttttacttgtgcctctttgtaagaacataccatgtgtaacttttttgtggcattaacatggactaattccttttgagtag

upper sequence: GLYMA16G03170.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 5
ATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgttcatgaggaattccttttctcactcaggttttttatgattatcttttgtctcatgttttaatatctgtgtccag
||||||||||| |||||||| ||||| |||||||| || || ||| | ||||| ||||| |  ||||| |||||||| || ||||||||||| || |||||||  |  ||  |    | |    | | ||||     || | ||||   |  | || || |   || ||  ||  |  |    
ATATCTGCTAGTATTGCTGGTGATATGGTTCTTGCAGCGGCCTATTCCCATGAACTGCCTCACTATGGGCTTGAAGTGGGTCTTACAAATTACGCGGCAGgtatatatttactctccattagtctatatcacc----ttctatatgtggaagtattctcactgcttctatcatgagcatag--

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|7041875|gb|AW471769.1|AW471769
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|21602194|gb|BQ612525.1|BQ612525
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|4436984|gb|AI522849.1|AI522849
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|192315894|gb|FK008595.1|FK008595
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|13252441|gb|BG363352.1|BG363352
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|6848438|gb|AW350728.1|AW350728
EST:     TGAGCTGCCACGATATNNNC-TGNAGTAGGGCTTANNNNNNATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCNTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|15336852|gb|BI497508.1|BI497508
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|4397465|gb|AI496462.1|AI496462
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|19268986|gb|BM885242.1|BM885242
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|192308475|gb|FK001377.1|FK001377
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|209701098|gb|BW664200.1|BW664200
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGTACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|192317627|gb|FK007581.1|FK007581
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|207837508|gb|GD809814.1|GD809814
EST:     CTTGAAGTTAGGGTCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: CTTGAAG-TAGGG-CTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|7233168|gb|AW568517.1|AW568517
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|151393465|gb|EV263340.1|EV263340
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|18040030|gb|BM308324.1|BM308324
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|7284984|gb|AW597471.1|AW597471
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|15814259|gb|BI786534.1|BI786534
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|192315893|gb|FK008594.1|FK008594
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|151412354|gb|EV282166.1|EV282166
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAG
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|42722855|gb|CK768754.1|CK768754
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
EST: gi|192317628|gb|FK007582.1|FK007582
EST:     TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAG                         CTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA
genomic: TGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgtt ... ctgtgtccagCTTATTGCACTGGTCTCCTGTTGGCCCGAAGAGTCCTCAAAACACTTGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTGAAGTAGGGCTTACAAATTATGCTGCAGgtactttgttcatgaggaattccttttctcactcaggttttttatgattatcttttgtctcatgttttaatatctgtgtccag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG