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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattctttctgcttgatattctattagggtttaaatttctttttcttttatgctgaccaatttttttcatgcag

Basic information

species Zea mays
transcript GRMZM2G011893_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011893_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g01410.1 (Oryza sativa), 5'ss of exon 6
AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc-------tttctgcttgatatt--ctattagggtttaaatttctttttcttttatgct-gaccaatttttttcatgcag-----------------------------------------------------
|||||| | ||||| |||||  |||| |||||||||||||||||||||||||||||||| || |||| | | ||  |||| ||| |||||||| || ||||| | |||||       ||| || ||   |||  ||  |   |||  | ||  |||  ||| ||  ||    ||| ||   |    |                                                       
AAAATGAGTGATGGGTGGGGGTTGGCTACTGATGGAAAAGTTCTTTTTGGCAGTGATGGTACTTCAAGGTTATACCAGCTTGATCCAAAGTCAATTCAAGgtaattattccagtgattttgtgattcccattggctcatgttgttcgacttgatttcacttctagactcaggcaacttgcctgggactaaaaactgttgtttgaaacttccattttgattatttgacattcttttggtgcag

upper sequence: GRMZM2G011893_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G24440.1 (Glycine max), 5'ss of exon 6
AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgtta--ctattc--------tttctgcttgatattcta---ttagggtttaaatttctttttctt-ttatgctgaccaatttttttcatgcag---------------------------------------------------------------------------
 | |||  ||| |||||||||||||| ||||||||||||||  | ||||| ||||||||||  ||||   ||||| |  | ||  |  |  || || ||||||   || | |        |     |||    ||  |   ||   ||  |||   ||||  |   | ||      | | ||||   |                                                                                
GATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTGAGCCTCAACCATTTAAAGgtttgtctgtccaatgaagttccacacttttcctttcactttttatgtgcaaacccctttcccaaatcatttgtgtccacttttcaaacttgaaaatactctgtttagtttatctctgtttgtcttgcattttcatggaatttacattgccctattggctgtacgtag

upper sequence: GRMZM2G011893_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA16G29760.2 (Glycine max), 5'ss of exon 6
AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattctttctgct-tgatattctattagggtttaaatttctttttcttttatgctgaccaatttttttcatg--cag------------------------------------------------------------------------
 | |||  |||||||||||||||||| |||||||||| | |  | ||||| ||||||||||  ||||   ||||| |  | ||| |  |  |  || ||||||  | |      ||   |  |||||  ||    |    |||| | |        |  |  | ||   ||||  ||  |||                                                                        
GATATGAAAGATGGTTGGGGTCTGGCAACTGATGGAACATTGTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAAATTGATCCTCAAACGTTTAAAGgtttgtctgtccaatgaagttctattcctttcctttcaccatttatgtgcaaaacctcattcctaaacctttttgtgtccagctttcaaacttgacaatacttagtgtttgctttgcattttcatggaacttaacattgccctctttcctgtag

upper sequence: GRMZM2G011893_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G24430.1 (Glycine max), 5'ss of exon 3
AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactat-tctttctgcttgatattctattagggtttaaatttctttttcttttatgctgaccaatttttttcatgcag-----------------------------------------------------------------------------
   |||  |||||||||||||||||| ||||||||||||||  | ||||| |||||||| |  ||||   ||||| |  | ||| |  |  || || ||||||  | | ||  |     |  |||||  ||    |    |||| | |           |  | ||   ||||   |  |                                                                             
GCTATGAAAGATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGTAGTTCAACATTGTATCAAATTGATCCTCAAACATTTAAAGgtttgtctgtccattgaagttctattcctttcctttcaccatttatgtgcaaagccccattcctaaacctttttgggtcgtcctgctttcaaacttgacaatgctttgtgtttgctttgaatttagatgaaacttaacactgctctcttttctgtag

upper sequence: GRMZM2G011893_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA09G24450.1 (Glycine max), 5'ss of exon 6
AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCA--CTTGAAGgttactattctttctgcttgatattctattagggtttaaatttctttttcttttatgctgaccaa---tttttttcatgcag----------------------------------------------------------------------------------
         ||||||||||||||||| ||||||||||||||  | ||||| ||||||||||  ||||   ||||| |  || ||||||| | |  ||   |  ||   |   || |   |||    || || | | |  |    | |  ||     ||  |  || |   ||||||   | |||                                                                                  
---------GATGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAAATG-ATTCAAACTGATCCTCAGACATTTAAAGgtttgccaattgcctgtcaatgaagttccattcctttcctttcaccattttttcccaaacttttttgggtccagttttctaacttgacaatactttgtttagttaatgtgtatgccttgcattttagtggaatttacattgccctattttctgtag

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|60352045|gb|DN219018.1|DN219018
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|78179760|gb|DV550133.1|DV550133
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60393994|gb|DN226864.1|DN226864
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|211290372|gb|FL395524.1|FL395524
EST:     AATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: AATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60348982|gb|DN215955.1|DN215955
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|8577165|gb|BE129802.1|BE129802
EST:     GCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: GCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|18964079|gb|BM660797.1|BM660797
EST:     CAGTCATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|78122303|gb|DV540687.1|DV540687
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60352117|gb|DN219090.1|DN219090
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|71428221|gb|DR809271.1|DR809271
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60350066|gb|DN217039.1|DN217039
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|60357511|gb|DN224484.1|DN224484
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|71446780|gb|DR827830.1|DR827830
EST:     CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAG                         TCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA
EST: gi|78122304|gb|DV540688.1|DV540688
EST:     CAGTGATGGCACCTCAGTGCTGTATAAGCTGGATTCAGAGTCACTTGAAG                         TCATGAAAGTGGTGAGTGTCAAGTATCACGGTAATCAACTCCTCTATCTTA
genomic: CAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTA

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: 130

AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 118

AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 165

AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattc ... tttcatgcagTCATGAAAGTGGTGACTGTCAAGTATCACGGTAATCAAGTCCCCTATCTTAATGAGCTGGAATATATAGATGGTGAAGTCTGGGCAAATGTCTGGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGGATTCAAAGTCACTTGAAGgttactattctttctgcttgatattctattagggtttaaatttctttttcttttatgctgaccaatttttttcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG