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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcatatgctttactacttgtcttctttgtcttaaagctttcttaagctgaacttgtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA

Basic information

species Zea mays
transcript GRMZM2G097995_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097995_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S365_37V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------gtaagatcatat--gctttactacttgtcttctttgtcttaaagctttcttaagctgaa----cttgtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA
                                ||   ||   ||  | |||       |  | || ||      | ||  ||    |||||    |||   || |||||||||||| || || |||||||| |  ||||||||||||||||| |||||       |                                          
gtatggattcatctttgcacatacgagtttccgtttcattgcattaggtttttagtccgcttcctgtgagagtcaactggctgttactgaaaccacttcgtcttgcagGAAATGGTGGACTTTCTTGTGGATGTATGGGAGCAAGAAGGCCTCTATGAAAGAAGATAA----------------------------------------
















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|6342791|gb|AW165615.1|AW165615
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|6431871|gb|AW172075.1|AW172075
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|32165086|gb|CD670404.1|CD670404
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|211490460|gb|FL154418.1|FL154418
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGC-TTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|32825283|gb|CD965005.1|CD965005
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|28910854|gb|CB331648.1|CB331648
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|211525931|gb|FL453813.1|FL453813
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|22472576|gb|BU037056.1|BU037056
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|29130525|gb|CB381229.1|CB381229
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|87156696|gb|DY401485.1|DY401485
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|31664502|gb|CD573435.1|CD573435
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|18171092|gb|BM340932.1|BM340932
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|87155503|gb|DY400292.1|DY400292
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|28909927|gb|CB331169.1|CB331169
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGC
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGC
EST: gi|31664503|gb|CD573436.1|CD573436
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGA
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGA
EST: gi|32792334|gb|CD944570.1|CD944570
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|32807750|gb|CD959984.1|CD959984
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAGGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|29543916|gb|CB604296.1|CB604296
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|211490455|gb|FL154413.1|FL154413
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|29543917|gb|CB604297.1|CB604297
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|31909751|gb|CD651076.1|CD651076
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
EST: gi|22472577|gb|BU037057.1|BU037057
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGC
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGC
EST: gi|29544694|gb|CB605074.1|CB605074
EST:     AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGC                         GAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT
genomic: AAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGAT

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: 120

TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 98

TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

TTGGAACACAACGTATGAAAGTCTGCTAGGAAGCAATAAGCCATTCTCCCAACCGATACCTCTTGGCgtaagatcat ... gtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactacttgtcttctttgtcttaaagctttcttaagctgaacttgtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA
                            tttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcatatgctttactacttgtcttctttgtcttaaagctttcttaagctgaacttgtactcgcagGAAATGGTAGATTTGCTTGTGGACGCTTGGGAGCAAGAAGGCCTTTATGATTAGGCCTGTGGAGTTCATTATTTGACTCGGATTAATCGCTTAATGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG