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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatattactcgatgagccattgctcccaatgtctagctctgcagtcttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgccagtgtcatacttctgaacattgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatag

Basic information

species Zea mays
transcript GRMZM2G031107_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031107_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g38840.2 (Oryza sativa), 5'ss of exon 11
CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatattactcgatgagccattgctcccaatgtctag--ctctgcagtcttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgccagtgtcatacttctgaacattgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatag
|||||||||||||||||||||||| |||| || ||||||||||||||||| ||||||||||||||| ||||| |||||||| |||| ||||||||||| |||| || |||| |  |    |||     |  || |  ||   | || ||||    |||| | ||  ||   |||||   ||| |   || | ||  | | ||  | |                                                                      
CAATATGATGGCTACAAGGATGACTCTACGGTACCAGATGACTCCAACACACCTACTTTTGCATCTCTTGTATTGAGGGTAAACAATGAAAGATGGGAAGgtatatgttacaccttacaacata----cagatatacagtattttgaagtcacttttaaacaaatatctgcattttc-caactg---aactgccttttttcgatacaa---------------------------------------------------------------------

upper sequence: GRMZM2G031107_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA16G06850.3 (Glycine max), 5'ss of exon 11
CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatattactcgatgagccattgctccc----aatgtctagctctgcagtcttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgccagtgtcatacttctgaacattgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatag
|||||||| ||||| || |||||||| || || || ||||| || |||||||| || |||||| ||||||| ||| |  ||||||| ||||||||||| ||| |  || |   | ||| |  || || ||    |      |   ||| ||  | | |||||      ||  |  |   | ||   |  || |   ||  |   ||||||  || | |  | | |   |  | |  | | | |||| |||| |   |                      
CAATATGAAGGCTATAAAGATGACCCAACCGTACCTGATGAGTCTAACACCCCAACATTTGCAACTGTTGTTCTGCGAATACACAATGAAAGATGGGAAGgtcag-atgaaatgttgaacatttccttcctaaaagaaataaatactgaagcttcctttaatt-----tctttggtgcaaaaattaggaaaat---acagtagttcatat-tcattctggtgcctaaaagaagtata-tatatattttttg-tatcag---------------------

upper sequence: GRMZM2G031107_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA19G22690.1 (Glycine max), 5'ss of exon 11
CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgta--aatattactcgatgagccattgctcccaatgtctagctctgcagtcttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgccagtgtcatacttctgaacattgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatag
|||||||| ||||| || ||||| || |||||||| ||  | || ||||| |||||||||||| ||||| | ||| | |||||||| ||||||||||||||||  |  || |  | || |  | ||  |||        |  | |||| | |   || |  | |   | |||       ||   || |  ||||  |  || | ||                                                                       
CAATATGAAGGCTATAAAGATGATCCAACTGTGCCTGACAATTCAAACACTCCTACTTTTGCAACTGTTATTCTGCGAGTACACAATGAAAGATGGGAGGgtatgagaataatgccatcaatc-tttttcctgtaagacaaatttgcattgtagattcagggcatg-ctatagg---gaaatttgagacctccc--ttggctttatt----------------------------------------------------------------------

upper sequence: GRMZM2G031107_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S192_39V6.4 (Physcomitrella patens), 5'ss of exon 11
CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatattactcgatgagccattgctcccaatgtctagctctgcagtc-ttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgcca-gtgtcatacttctgaacattgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatag
|| ||||| ||||||||||||||||  ||||| ||| |||| |||  ||| ||||||||||||||| |||| |||    |  |||| ||  | ||||| ||||   |||  |  |  |  |||        || |  |    || |||| ||  ||      |  |      ||||| ||     | | |   |||   | |  | |   |  |    |   | | |   |||||                                          
CAGTATGAGGGCTACAAGGATGACCAGACTGTTCCAAATGATTCCTCCACTCCTACTTTTGCATCTCTTGTGCTGCACATCAACAATGAGCGTTGGGATGgtattcattttttaactaaacat--------at-tgcaatcttgtagtcatttgtttgcttgattttatgggttttagaaagaattgaattgtacttatccttttttctgatatacgttgtcttttattgttgcag-----------------------------------------

upper sequence: GRMZM2G031107_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S222_130V6.3 (Physcomitrella patens), 5'ss of exon 11
CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatattactcga-tgagccattgctcccaatgtctagctctgcagtcttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgccagtgtcatacttctgaacat-tgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatag
|| ||||| |||||||| |||||||||||||| ||| |||| |||  ||| ||||||||||||||| |||| ||  |  |  |||||||| | ||||| ||||   |||  |  | ||| |  |||||  |    |  | | || |  | || | | || ||   |   |||||||||       | |||   | | |   |  ||||  |   || |   | | |   |     || ||| || |    || | | | ||                
CAGTATGAGGGCTACAAAGATGACCCTACTGTTCCAAATGATTCCGTCACTCCTACTTTTGCATCTCTTGTTCTTCGCATCAACAACGAACGGTGGGATGgtatgcatttttgaactgaacacttgctttct---tacaacgcttc--ttttgcgtgataga-tttttttatttttat-------ttattt--attttattttttatgtgaagatc-tggatttaactgtacttgatcttttttttaacttgatgattccag---------------

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|14203621|gb|BG837298.1|BG837298
EST:     CCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGG                         GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTTAATTCGAGGAAAGCAG
genomic: CCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG
EST: gi|71596396|gb|DR907147.1|DR907147
EST:     CGAAAGATGGGAGG                         GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG
genomic: CGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG
EST: gi|78077421|gb|DV505855.1|DV505855
EST:     CCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGG                         GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG
genomic: CCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG
EST: gi|18661166|gb|BM501251.1|BM501251
EST:     CCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAAGG                         GGGTCCCAT-CATCCTCAANGCTGGCAAAGCACTAAATTCGAGGAAAGCA
genomic: CCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGA-GGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCA
EST: gi|76281884|gb|DV021452.1|DV021452
EST:     CCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGG                         GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG
genomic: CCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG
EST: gi|78109019|gb|DV527436.1|DV527436
EST:     CCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGG                         GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG
genomic: CCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAG

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: 106

CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 542

CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 595

CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 196

CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatatta ... tgtcgcatagGGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATATGATGGCTACAAGGATGACCCTACTGTGCCAGATGACTCCAACACCCCTACTTTTGCATCTGTTGTACTGAGGGTACACAACGAAAGATGGGAGGgtaaatattactcgatgagccattgctcccaatgtctagctctgcagtcttccttaatcgaacctccatatttttataaccggataattcccactctgcgtcatatgccagtgtcatacttctgaacattgcaatgtttattctttggtgctaaatgcaaatgactgtcgcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG