Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatggtcctgttcctcatctcttcattaatttcttaaggatgctgaactgtggaatttcttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG

Basic information

species Zea mays
transcript GRMZM2G177914_T02
intron # 2
splice site 3'
intron type U2

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|19822213|gb|BQ048237.1|BQ048237
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211469618|gb|FK972985.1|FK972985
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211469620|gb|FK972987.1|FK972987
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211467096|gb|FK972975.1|FK972975
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211469627|gb|FK972994.1|FK972994
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGG
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGG
EST: gi|211469622|gb|FK972989.1|FK972989
EST:     CCACCCGAGAAGCATCAGGACCTCGTC-GCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAG
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAG
EST: gi|211469619|gb|FK972986.1|FK972986
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211467101|gb|FK972980.1|FK972980
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGGAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211467098|gb|FK972977.1|FK972977
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211467097|gb|FK972976.1|FK972976
EST:     CCACCCGAGAAGCATCAGGACCTCGTC-GCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGA
EST: gi|211467089|gb|FK972968.1|FK972968
EST:     CCACCCGAGAAGCATCAGGACCTCGTC-GCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGATGAGCGCGA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGA-GAGCGCGA
EST: gi|211472153|gb|FK973002.1|FK973002
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211472152|gb|FK973001.1|FK973001
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211472150|gb|FK972999.1|FK972999
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211467094|gb|FK972973.1|FK972973
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACT
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACT
EST: gi|26455836|gb|CA827419.1|CA827419
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAG
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAG
EST: gi|211469626|gb|FK972993.1|FK972993
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|76011356|gb|DT938526.1|DT938526
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211469628|gb|FK972995.1|FK972995
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211472147|gb|FK972996.1|FK972996
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
EST: gi|211469614|gb|FK972981.1|FK972981
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGG
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGG
EST: gi|71429421|gb|DR810471.1|DR810471
EST:     CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAAT                         TACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA
genomic: CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCA

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), 47 (downstream exon)
Score: 122

CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 184

CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 196

CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 150

CCACCCGAGAAGCATCAGGACCTCGTCCGCTGTGTCTTCCAATgtatgcatgg ... cttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatctcttcattaatttcttaaggatgctgaactgtggaatttcttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG
          cattaat  putative branch site (score: 150)
                                          tttcttgtt  putative PPT
        ttcattaatttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatggtcctgttcctcatctcttcattaatttcttaaggatgctgaactgtggaatttcttgttacagTACTCTCTGCAAGGCCCGAGAGCGCGAGCAATTTTGTCAAGGTGGACTCCATCTTTGGCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA