Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgctttttttttgtttcttatagcttgcaacctaccaaggcaatttatgaatgatagtaggcctattacttaactagcaccttttctag

Basic information

species Zea mays
transcript GRMZM2G022859_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022859_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 3
GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgctttttttttgtttcttatagcttgcaacctaccaaggcaatttatgaatgatagta--ggcctattacttaactagcacc-ttttctag
||| ||| |||| ||||||||||| |||||||| | |||||| ||||| |||||||||||||| ||||||||| |||||||||| |||||||||||| ||||||  || |  ||  |||    |||  ||||           || | | ||  ||||| ||  ||  ||| || ||||||    |  |   |||||||
GTTGAAGTTGTTCTGTGATACAGACTATCCAGACAGACCACCTACTGTTCGATTCCAGACTCGAATCAATATGTCATGTGTGAATCAAGAAACTGGAATGgtacatgtccacttgcttt---cctttaagct-----------aaagtagttggtgaatcattttattggcgtagtacttacaaggagctactttctag

upper sequence: GRMZM2G022859_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G35000.1 (Glycine max), 5'ss of exon 3
GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgctttttttttg---tttcttatagcttgcaacctaccaaggcaatttatgaatgatagtaggcctattacttaactagcaccttttctag
| | ||  | |||||||  |  ||||||||||| || ||||| |||||  |||| |||||| |||| || ||||| ||||| ||||||||||||||| |||||       ||||   |     || ||| || ||||  |   |    |  || |||| |||      |   | |                        
GCTGAAATTATTTTGTGGCAAGGATTATCCAGACAATCCACCAACTGTTAGATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaacattttcactaaggattccttgta-cttgtgattgaatttg--aacttataaatatctaaattaccag-----------------------

upper sequence: GRMZM2G022859_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G04710.1 (Glycine max), 5'ss of exon 3
GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgctttttttttg---tttcttatagcttgcaacctaccaaggcaatttatgaatgatagtaggcctattacttaactagcaccttttctag
| | ||  | |||||||  |  ||||||||||| || ||||| |||||  |||| |||||| |||| || ||||| ||||| ||||||||||||||| |||||       ||||         || ||| || ||||  |   |    |  || |||| |||      |   | |                        
GCTGAAATTATTTTGTGGCAAGGATTATCCAGACAATCCACCAACTGTTAGATTTCAGACTAGGATTAACATGACTTGTGTCAACCAAGAAACTGGAGTGgtaggtaacattttcacaaaggattccttgta-cttgtgattgaatttg--aacttataaatatctaaattaccag-----------------------

upper sequence: GRMZM2G022859_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 5'ss of exon 3
GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgctttttttttgtttcttatagcttgcaacctaccaaggcaatttatgaatgatagtaggcctattacttaactagcaccttttctag
||| || ||||| |||| |   || ||||| ||||| ||||| |||||    |||||||||||||| |||||||| ||||| || || ||||||||| ||||        ||  |||       || ||   ||     |     |  |||      ||||| ||     ||  |                     
GTTGAAACTGTTCTGTGGTCAGGACTATCCGGATAATCCACCAACTGTGAAGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaattttactttcaagaatttttatgctgtggtatgttt-gataataagcttatgatggtcaaattaccag--------------------

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|71423683|gb|DR806127.1|DR806127
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211292704|gb|FL181548.1|FL181548
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|14243209|gb|BG840922.2|BG840922
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|60345888|gb|DN212861.1|DN212861
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|88754530|gb|DY538671.1|DY538671
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211187611|gb|FL186089.1|FL186089
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|33100243|gb|CF060203.1|CF060203
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211292709|gb|FL181553.1|FL181553
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211292700|gb|FL181544.1|FL181544
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|60337925|gb|DN204898.1|DN204898
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211292707|gb|FL181551.1|FL181551
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|71423686|gb|DR806128.1|DR806128
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|13389071|gb|BG462542.1|BG462542
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|76016546|gb|DT943716.1|DT943716
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211292705|gb|FL181549.1|FL181549
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211292703|gb|FL181547.1|FL181547
EST:     ATTCCAGACTCGYGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTA
genomic: ATTCCAGACTCG-GATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTA
EST: gi|78025429|gb|DV493816.1|DV493816
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|16379365|gb|BI992896.1|BI992896
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211292701|gb|FL181545.1|FL181545
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|76913969|gb|DV165351.1|DV165351
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211343001|gb|FL470860.1|FL470860
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|60350937|gb|DN217910.1|DN217910
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|14242746|gb|BG840531.2|BG840531
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211241891|gb|FL451480.1|FL451480
EST:     TATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211185218|gb|FL186081.1|FL186081
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTCGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211185222|gb|FL186085.1|FL186085
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTCGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|60351107|gb|DN218080.1|DN218080
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|60350383|gb|DN217356.1|DN217356
EST:     GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
EST: gi|211292710|gb|FL181554.1|FL181554
EST:     TATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTG                         GTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG
genomic: GATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACGATGGAGGACATTCTGACCAGCTTAAAAAGGGAGATGTCAACTCCACAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 134

GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACGATGGAGGACATTCTGACCAGCTTAAAAAGGGAGATGTCAACTCCACAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACGATGGAGGACATTCTGACCAGCTTAAAAAGGGAGATGTCAACTCCACAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgc ... ccttttctagGTTGAACCAAGTCTATTTCCTATGCTTGGAAAGTGGGAAAGGGAACATACGATGGAGGACATTCTGACCAGCTTAAAAAGGGAGATGTCAACTCCACAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAAAGCTGTTTTGTGATACAGATTATCCAGATAAACCACCGACTGTCCGATTCCAGACTCGGATCAATATGACATGTGTGAACCAAGAAACTGGATTGgtactcgtgctttttttttgtttcttatagcttgcaacctaccaaggcaatttatgaatgatagtaggcctattacttaactagcaccttttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA