Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtagtcagactcaagatccttctagttttgactttcatttatgtttgaataactgcctgatgtcatttctctctttaactttacataaaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGTTCCGTCGGGAATATGAGATGCGCAGAATGAAACAG

Basic information

species Zea mays
transcript GRMZM2G057251_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057251_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g48020.1 (Oryza sativa), 3'ss of exon 3
-----tgtgtagtcagactcaagatccttctagttttgactttcatttatgtttgaataactgcctgatgtcatttctctctttaactttacataaaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGTTCCGTCGGGAATATGAGATGCGCAGAATGAAACAG
     | | |  |||        ||  | ||  |     ||||  ||  |  |     |   |||    |        || |    |||  ||     ||||||||||| |||||||||||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||||| ||||||||||
tttcttttctcatcatttcgggcatgatcctgttagatgcttttgttggtcctcttgaaggagccatgagctgacctactttcccgcttgcca-----catacagATGGCAACTTTGATGATGAGTACTTTAAGGGAACAGAAGAATCAAATCAGTTTCGTCGGGAATATGAGATGCGCAAAATGAAACAG
















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|32827428|gb|CD967106.1|CD967106
EST:     GATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTT
genomic: GATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTT
EST: gi|78082805|gb|DV511198.1|DV511198
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|74237329|gb|DT645243.1|DT645243
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|60400857|gb|DN233664.1|DN233664
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|71770367|gb|DR968304.1|DR968304
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|76936954|gb|DV174978.1|DV174978
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTATTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|60338253|gb|DN205226.1|DN205226
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTATTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|78076770|gb|DV505204.1|DV505204
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|76018601|gb|DT945771.1|DT945771
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|78074902|gb|DV503336.1|DV503336
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTATTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|91869751|gb|EB400522.1|EB400522
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|78076771|gb|DV505205.1|DV505205
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|60397948|gb|DN230764.1|DN230764
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|149088922|gb|EE178063.2|EE178063
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|211444699|gb|FL108662.1|FL108662
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|60400044|gb|DN232851.1|DN232851
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|32809053|gb|CD961287.1|CD961287
EST:     GATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTAC
genomic: GATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTAC
EST: gi|74237328|gb|DT645242.1|DT645242
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|211515339|gb|FL131682.1|FL131682
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGGAACTTTGATGATGAGTATTTTAAGGGGACAGAA
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAA
EST: gi|71299507|gb|DR785763.1|DR785763
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|32808361|gb|CD960595.1|CD960595
EST:     GATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTA
genomic: GATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTA
EST: gi|76018600|gb|DT945770.1|DT945770
EST:     AGCCTCAGGATCTCGCACGGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|211515335|gb|FL131678.1|FL131678
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTATTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|78082804|gb|DV511197.1|DV511197
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|67038186|gb|CO464516.1|CO464516
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|32857817|gb|CD997498.1|CD997498
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|78086622|gb|DV515015.1|DV515015
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|74235878|gb|DT643792.1|DT643792
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|148932647|gb|EC876561.2|EC876561
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|211444700|gb|FL108663.1|FL108663
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTAC
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTAC
EST: gi|15313737|gb|BI478932.1|BI478932
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|76281470|gb|DV021038.1|DV021038
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|149015005|gb|EE044748.2|EE044748
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
EST: gi|149070317|gb|EE158717.2|EE158717
EST:     AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTG                         ATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT
genomic: AGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGT

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: 48 (upstream exon), 47 (downstream exon)
Score: 253

TCAATCCCAGATGGTAGTTCTACTGCCACAAAGAAAAATGGAAGTTGGGGAGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGTTCCGTCGGGAATATGAGATGCGCAGAATGAAACAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 383

TCAATCCCAGATGGTAGTTCTACTGCCACAAAGAAAAATGGAAGTTGGGGAGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGTTCCGTCGGGAATATGAGATGCGCAGAATGAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

TCAATCCCAGATGGTAGTTCTACTGCCACAAAGAAAAATGGAAGTTGGGGAGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGTTCCGTCGGGAATATGAGATGCGCAGAATGAAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 330

TCAATCCCAGATGGTAGTTCTACTGCCACAAAGAAAAATGGAAGTTGGGGAGCCTCAGGATCTCGCACTGGAGGAGCCATAAAGTTCGACTCTACTGCTGgttagtgagc ... aaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGTTCCGTCGGGAATATGAGATGCGCAGAATGAAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgaataactgcctgatgtcatttctctctttaactttacataaaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGTTCCGTCGGGAATATGAGATGCGCAGAATGAAACAG
                               tttaactttacataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtagtcagactcaagatccttctagttttgactttcatttatgtttgaataactgcctgatgtcatttctctctttaactttacataaaacatacagATGGAAACTTTGATGATGAGTACTTTAAGGGGACAGAAGAATCTAATCAGTTCCGTCGGGAATATGAGATGCGCAGAATGAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - -tttcatt
- - - - - - - - - - - - - - - - - - - - - -atgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgatg