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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattcaaaatgcgcacctcatactacttttgtttatgctacactgtagactgctagcagaggtagtgttctcatttccatttttctctctctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAG

Basic information

species Zea mays
transcript GRMZM2G014066_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014066_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g48190.1 (Oryza sativa), 3'ss of exon 2
cattcaaaatgcgcacctcatactacttttgtt--tatgctacac-tgtagactgctagcagaggtagtgttctcatttccatttttctctctctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAG
  |||||| |            |  ||| ||||  |||  |   | | || | ||      | | |  | | || ||||  ||||   |  || |  ||||||||||| ||||| |||| | ||| | |||||||||||||| | || ||||| |||||||| ||||||||| ||||||||
-gttcaaagtatattaaatcagcaccttatgttcatatattgtgcatataaaatgtgcattgtgttcttctcctgattt--atttgctttgctttgctttcagCCCTGTCCCATCTGCTTCGAAAAGATTACAAGAGATATGTTAAATCATATCACCATGCAACATGGTTACTTGTTCAAG
















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|74239572|gb|DT647486.1|DT647486
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|71305275|gb|DR788771.1|DR788771
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|149104466|gb|EE289912.2|EE289912
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCCAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|71422365|gb|DR805702.1|DR805702
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|149086120|gb|EE175660.2|EE175660
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|94472198|gb|EB701156.1|EB701156
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|148958296|gb|EC904516.2|EC904516
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|148990777|gb|EE032191.2|EE032191
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|89250646|gb|DY622432.1|DY622432
EST:     CCCTCTGCGTCCCCCTCGAGGAGGACCACCCCTATGAGCCCCCCTCCGCG                         CCCTGCCCCATTTGCTCCCCAAGGGTTACAAGAGATATGCTTAAACC-TAT
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAA-CCATAT
EST: gi|18654784|gb|BM499589.1|BM499589
EST:     AGGAGGACCACCCCTATGAGCCCCACTCCGGG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: AGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|71427572|gb|DR808622.1|DR808622
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|20300095|gb|BQ163038.1|BQ163038
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|18963077|gb|BM660226.1|BM660226
EST:     GGAGGACCA-CCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: GGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|87152622|gb|DY397411.1|DY397411
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|211484735|gb|FL156869.1|FL156869
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|89247987|gb|DY619773.1|DY619773
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|149108982|gb|EE293079.2|EE293079
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
EST: gi|76936894|gb|DV174950.1|DV174950
EST:     CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCG                         CCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG
genomic: CCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATG

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), 48 (downstream exon)
Score: 25

GTGGCCGGATGTCGCCTGCCCCTACTGCTACGAGGACCATGACGTCGCGTCCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

GTGGCCGGATGTCGCCTGCCCCTACTGCTACGAGGACCATGACGTCGCGTCCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 50

GTGGCCGGATGTCGCCTGCCCCTACTGCTACGAGGACCATGACGTCGCGTCCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 54

GTGGCCGGATGTCGCCTGCCCCTACTGCTACGAGGACCATGACGTCGCGTCCCTCTGCGTCCACCTCGAGGAGGACCACCCCTATGAGCCCCACTCCGCGgtgagtcagt ... ctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagactgctagcagaggtagtgttctcatttccatttttctctctctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAG
                    tgttctcatttccatt  CT-rich tract
                                 atttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattcaaaatgcgcacctcatactacttttgtttatgctacactgtagactgctagcagaggtagtgttctcatttccatttttctctctctcatttcagCCCTGCCCCATTTGCTCCCAAAGGGTTACAAGAGATATGCTTAACCATATGACCATGCAGCATGGTTACCTGTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
cattcaa
- - - - - - gcacctc
- - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - gctacac
- - - - - - - - - - - - - - - - - - - - - - - - - tgctagc