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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaataacagtttcactttttttaaaaatgttttaaattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG

Basic information

species Zea mays
transcript GRMZM2G162672_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 3'ss of exon 11
gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaataaca--gtttcactttttttaaaaatgttttaaattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
||| | ||  | | | | ||||| |   ||||||    | |  |    | |  ||  |     |  |  |  | |    ||    ||||  ||||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||| |||||||
gttcttcttctgtctgtagtgtagag--ttatcacagcccttttctgtagttccaaagaaaagcaatcatccatatcacttaccttttttcagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g28200.2 (Oryza sativa), 3'ss of exon 10
----gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaata-----acagtttcactttttttaaaaatgttttaaattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
     | |   |||| || | | ||||        | || |  |  ||| ||  ||     | ||     |  |  |  | |    ||    ||||  ||||||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| || ||||||||||| |||||||
gggcttcaggttcttcttctgtctgtagtgtagagttatcacagcccttttctgtagttccaaagaaaagcaatcatccatatcacttaccttttttcagTCACTCCCGGTTGCTTTTGGTATGGAAACTGCAAAGTGGATATGTGTAGGAGCGATTGACATAACTCAATTATCCGTTGCAG

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 11
--------------------------------------gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaataacagtttc-actttttttaaaaatgttttaaattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
                                        |   ||  ||  | || |  ||||  | |||||  ||   | |   | || |   | |    |||| ||         |   ||  |||||| ||||| |||||||||||    ||||||||||| ||||| |||||||| || ||||| || || ||||||||||| ||  
ggtatactctattgtcctttgcctttcaataacagtactctgagcttattcatgttttagaaattctaatcatgtacagtcattgaagtagcttctactgacttttctattggctaccttctttgagtaGTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATCTGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCG-

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 3
-------------------------------------gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaataacagtttcactttttttaaaaatgttttaaatttt---gtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
                                       |  |||| ||  | || |  ||||  | |||||  ||   | |   | || |  ||  |||   |||   | ||  |    | ||   |||||| ||||| |||||||||||    ||||||||||| ||||| |||||||| || ||||| || || ||||||||||| || |
gtctactctattgtcctttgcctttcaataacagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagc--ttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTGCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G18470.1 (Glycine max), 3'ss of exon 11
-------------------------------------gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaataacagtttcactttttttaaaaatgttttaaatttt---gtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
                                       |  |||| ||  | || |  ||||  | |||||  ||   | |   | || |  ||  |||   |||   | ||  |    | ||   |||||| ||||| |||||||||||    ||||||||||| ||||| |||||||| || ||||| || || ||||||||||| || |
gtctactctattgtcctttgcctttcaataagagtactctgaactcattcatgttttagaaattctaatcatgtacagtcattaaagtagc--ttctactgacttttgtattggctaccttctttgagtagTCTCTTCCAGTTGCTTTTGGTTCTGAAACTGCAAAGTGGATATGTGTTGGCGCTATTGACATTACACAATTATCTGTAGCTG

upper sequence: GRMZM2G162672_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv08s0105g00590.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaataacagtttcactttttttaaaaatgttttaaattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
                               || |   |||| |  |||   ||||||   |||| | ||     | |  |||  ||||  |    |||  |   |  ||    ||    |||| || || || || |||||    |||||||| |||||||||||||| || || ||||| |||||||| ||||| || || |
gtttttcctgtctcttttacatgtttgcaatgtgaatatcttatccttttactaaata---atcaatcacacatatat--atagtagttgtaaccatttctatggtaattctgtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGTGCTATTGACATCACTCAGTTATCAGTGGCTG

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|211036110|gb|FL230102.1|FL230102
EST:     ATTGAAGGGGATAGGACTTTGGGGCTTCAT                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: ATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|71759623|gb|DR957560.1|DR957560
EST:     TAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|32940940|gb|CF045759.1|CF045759
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGACTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|211036106|gb|FL230098.1|FL230098
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|71314948|gb|DR794088.1|DR794088
EST:     AAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: AAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|211036107|gb|FL230099.1|FL230099
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|78120047|gb|DV538431.1|DV538431
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|71324982|gb|DR799184.1|DR799184
EST:     TGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|149110076|gb|EE293890.2|EE293890
EST:     AAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: AAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|166416781|gb|EG172855.1|EG172855
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCAACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGG
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCA-CTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGG
EST: gi|71426127|gb|DR807177.1|DR807177
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|71763867|gb|DR961804.1|DR961804
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|149080582|gb|EE169625.2|EE169625
EST:     TGTAAATGATTTTCA-GAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTT
genomic: TGTAAATGATTT-CAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTT
EST: gi|32931186|gb|CF035998.1|CF035998
EST:     ATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: ATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|32940989|gb|CF045808.1|CF045808
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
EST: gi|148929759|gb|EE285358.2|EE285358
EST:     TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAG                         TCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA
genomic: TTGTAAATGATTTCAAGAGTATTGAAGGGGATAGGACTCTGGGGCTTCAGgttatactct ... aattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacgtgcttctcaataacagtttcactttttttaaaaatgttttaaattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG
           caataac  putative branch site (score: 2)
            aataacagtttcactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatactctttttttttgtgtaaatatttatcattaacgtgcttctcaataacagtttcactttttttaaaaatgttttaaattttgtagTCACTTCCTGTTGCTTTTGGGATGGAAACTGCAAAATGGATTTGTGTTGGAGCAATTGATATCACTCAATTATCTGTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA