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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttcagtggcctgtttgatatgatgtaacatcattgtcatggaatgttcttggctaacataacatactcaattatcagatcctgaattgaaacaccatgtttgtttttatttgatgaatgatgtcgcttattgctatactgtgcaaagtttaccactatggcgctaaccgcgttgtttatgcatccag

Basic information

species Zea mays
transcript GRMZM2G166345_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166345_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g60660.2 (Oryza sativa), 5'ss of exon 9
GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttcagtggcctgtttgatatgatgtaacatcattgtcatggaatgttcttggctaacataacatactcaattatcagatcctgaattgaaacaccatgtttgtttttatttgatgaatgatgtcgcttattgctatactgtgcaaagtttaccactatggcgctaaccgcgttgtttatgcatccag
||||||||||||||| ||||||||||| ||||| ||||| || ||||| |||||||| || ||||||  |||   |  ||  |  | |||  | |  ||| ||  || |    | || ||  ||   |  |   ||   ||||      |||    |  | ||| || |  ||                                                                                    
GTTTGATGGGAAGCCAGAAGATGTTCTTAATCCGAAGAAGAAACAGCTCGACAAGATCACACCGgtatgctt---ttaccaatgcgctat--ttttgcatgatgctc-taagttatttttcccttttagcaatcacatgattagtctgccct----tccagcacaatctgggtg-----------------------------------------------------------------------------------
















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|4874363|gb|AI673883.1|AI673883
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|4573130|gb|AI586779.1|AI586779
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTCCCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|12972445|gb|BG267985.1|BG267985
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATGCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCAT-CTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTT
EST: gi|33098108|gb|CF058068.1|CF058068
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|211244774|gb|FL481676.1|FL481676
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|33095166|gb|CF055160.1|CF055160
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACC
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACC
EST: gi|213173994|gb|FM188956.1|FM188956
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|4628469|gb|AI619343.1|AI619343
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|71772536|gb|DR970467.1|DR970467
EST:     CAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|89247315|gb|DY619101.1|DY619101
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|18173735|gb|BM349123.1|BM349123
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|37381901|gb|CF627857.1|CF627857
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|33095762|gb|CF055756.1|CF055756
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|5005650|gb|AI711712.1|AI711712
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|91873662|gb|EB403619.1|EB403619
EST:     CTGAAGATGTTTTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTTGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
EST: gi|211165085|gb|FL207333.1|FL207333
EST:     CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCG                         CATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT
genomic: CTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTT

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: 240

GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTTACTACATCAGCTGGCCCATGTAGATCTTCGATTCACAACGGAAATGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTTACTACATCAGCTGGCCCATGTAGATCTTCGATTCACAACGGAAATGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTTACTACATCAGCTGGCCCATGTAGATCTTCGATTCACAACGGAAATGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttca ... atgcatccagCATCTTCGTACCGACGAGAATGGAATTGCAATGTTCAAAGGTGTTCCCTTTACTACATCAGCTGGCCCATGTAGATCTTCGATTCACAACGGAAATGTTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGATGGGAAGCCTGAAGATGTTCTAAATCCAAAGAAAAAGCAGCTGGACAAGATTACCCCGgtacacttcagtggcctgtttgatatgatgtaacatcattgtcatggaatgttcttggctaacataacatactcaattatcagatcctgaattgaaacaccatgtttgtttttatttgatgaatgatgtcgcttattgctatactgtgcaaagtttaccactatggcgctaaccgcgttgtttatgcatccag

- - - - - - - CTGAAG
- - - - - - -  TGAAGA
- - - - - - - -  AAGATG
- - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - -  GCTGGA