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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctggattatataatctagagagattataatctgaaacaaacaggaccttagtattactttcgtgatctctgctgacagatgacatgctccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGGTTGAATCAAAAGTTTTCTCTTAGCCACAGGTAAGATCATTACATAAG

Basic information

species Zea mays
transcript GRMZM2G043983_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043983_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 3'ss of exon 1
----------tgctggattatataatctagagagattataatctgaaacaaacaggaccttagtattactttcgtgatctctgctgacagatgacatgctccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGGTTGAATCAAAAGTTTTCTCTTAGCCACAGGTAAGATCATTACATAAG
          || |   || |   ||  |      ||   |||||||       |  | | |  ||| |||| ||||  |         | |||||| |||| |||  |||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| || ||||| ||||| || || ||||||||                  
ttgtgcgatttgatctgttgttgcatacatgctattttctatctgaattt--tggctcttgaacatttcttttgtgagttt--------gctgacattctccattttcagTGTCGTTGAAACCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACTAAAGGATTAAATCAGAAGTTCTCACTCAGCCACAG------------------
















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|211318724|gb|FL359237.1|FL359237
EST:     CAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|148982521|gb|EE028361.2|EE028361
EST:     CAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
EST: gi|211520444|gb|FL249049.1|FL249049
EST:     AACCTCCNTCTGCCC-GTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAAGATTGAGGTTTGACTTCACAAA
genomic: AACCTCC-TCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAA
EST: gi|78089042|gb|DV517435.1|DV517435
EST:     CAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCA                         TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG
genomic: CAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAG

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), 48 (downstream exon)
Score: 272

CCGCAGACGTCAGTGGGAGAGGAGAAGAAGGAGGAGAAGGTGGACTACCTCAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGGTTGAATCAAAAGTTTTCTCTTAGCCACAGGTAAGATCATTACATAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 55

CCGCAGACGTCAGTGGGAGAGGAGAAGAAGGAGGAGAAGGTGGACTACCTCAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGGTTGAATCAAAAGTTTTCTCTTAGCCACAGGTAAGATCATTACATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

CCGCAGACGTCAGTGGGAGAGGAGAAGAAGGAGGAGAAGGTGGACTACCTCAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGGTTGAATCAAAAGTTTTCTCTTAGCCACAGGTAAGATCATTACATAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 78

CCGCAGACGTCAGTGGGAGAGGAGAAGAAGGAGGAGAAGGTGGACTACCTCAACCTCCTCTGCCCCGTGCCCTTCGAGGAGATCCAGCGCGAGGCTCTCAgtttgtcccc ... ccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGGTTGAATCAAAAGTTTTCTCTTAGCCACAGGTAAGATCATTACATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccttagtattactttcgtgatctctgctgacagatgacatgctccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGGTTGAATCAAAAGTTTTCTCTTAGCCACAGGTAAGATCATTACATAAG
                          tgctgac  putative branch site (score: 78)
                                         tgctcctttt  putative PPT
        tattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctggattatataatctagagagattataatctgaaacaaacaggaccttagtattactttcgtgatctctgctgacagatgacatgctccttttgtagTGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGGTTGAATCAAAAGTTTTCTCTTAGCCACAGGTAAGATCATTACATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA