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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtagagtcaaacagaactctaatatcgtgcaatggaaatatcatgagaacttatcattctttctgttttgttcag

Basic information

species Zea mays
transcript GRMZM2G106213_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os09g12660.2 (Oryza sativa), 5'ss of exon 7
CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtagagtcaaacagaactctaatatcgtgcaatggaaatatcatgagaactta-tcattctttctgttttgttcag
|||||||||||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||||||||| |||||||||||||||||||||| |||||||| || |   ||||   ||| || ||| ||| | |||   | |  || ||||||| |  | |||| ||||  |     
CATTGCACAATCAACCATTCTGTGGTTGGACTCCGGTCCTGTATATCTGAAGGCGCAGTGATAGAGGACTCTCTGCTAATGGGTGCAGACTATTATGAGgtaaaataaaacaaaactatactatattatggtgtattgg---tgttgtgggaacttaattgtgctttttgttcag-----

upper sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 5'ss of exon 6
CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtagagtcaaacag--aactctaatatcgtgcaatggaaatatcatgagaacttatcattctttctgtt--ttgttcag----
 | |||| |||  |||| || || |||||||||||||||||||| || ||||||||  |||| || || || ||  ||||||| || || ||||||||||||||     |||   ||   ||   |  |     | ||||  ||  |  |||  | |  |  |  | | || |  |||||       
AACTGCAAAATTCATCACTCTGTGGTTGGACTCCGTTCCTGCATATCAGAAGGTGCTATTATTGAAGATTCGTTATTAATGGGAGCTGATTATTACGAGgtaaaaatctgtcttgcaatcaatcttcttgctaagtaatgtcaaccttttgatga-tggtggtcttctttgatgattgtttgcctag
















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|60337923|gb|DN204896.1|DN204896
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|31356186|gb|CD440543.1|CD440543
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|31357016|gb|CD441373.1|CD441373
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|32929383|gb|CF034195.1|CF034195
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGTAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|32934685|gb|CF039497.1|CF039497
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGTAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|67042108|gb|CO468363.1|CO468363
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|71301127|gb|DR786596.1|DR786596
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|32846616|gb|CD986297.1|CD986297
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGTAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGC
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|6918472|gb|AW400002.1|AW400002
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|110511027|gb|EE019293.1|EE019293
EST:     GGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: GGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|148950460|gb|EC896030.2|EC896030
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|78180055|gb|DV550428.1|DV550428
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|60352415|gb|DN219388.1|DN219388
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|37381963|gb|CF627890.1|CF627890
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|32856251|gb|CD995932.1|CD995932
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGTAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|32929486|gb|CF034298.1|CF034298
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGTAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|12046285|gb|BF728424.1|BF728424
EST:     AGGTGCCAG-TATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AGGTG-CAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT
EST: gi|211186265|gb|FL114940.1|FL114940
EST:     AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAG                         ACTGAGAATGATAAGAATGCCCTTTCTGAGACTGGTGGCATTCCCATTGGT
genomic: AAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGT

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: 647

CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTC


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 177

CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTC


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 25

CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 211

CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtaga ... ttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGCACAATCAATCATTCCGTAGTTGGACTCCGTTCCTGCATTTCTGAAGGTGCAGTTATAGAGGACTCTTTGCTAATGGGTGCAGACTATTACGAGgtaaagtagagtcaaacagaactctaatatcgtgcaatggaaatatcatgagaacttatcattctttctgttttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA