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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatcttattgaatttgtattttgacttatttatattaatgtggttggcacgtgatgaattctttgcctatccctctgaacttctgatgcag

Basic information

species Zea mays
transcript GRMZM2G134770_T03
intron # 6
splice site 5'
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|71428348|gb|DR809398.1|DR809398
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|32943442|gb|CF048261.1|CF048261
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|94474683|gb|EB703641.1|EB703641
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|78112738|gb|DV531132.1|DV531132
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|32841271|gb|CD980952.1|CD980952
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|166684106|gb|EG131653.1|EG131653
EST:     ATTCTCAGAAGAAGTCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: ATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|32839908|gb|CD979589.1|CD979589
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|6021134|gb|AW066062.1|AW066062
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAG                         GAGCTGGCCGNGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|88752563|gb|DY536704.1|DY536704
EST:     CACGAGAGCTGGCTCATATTTTGATGAAGATTCTCAGAAGAAGTCTGCAG                         GAGCGGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|32841323|gb|CD981004.1|CD981004
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|32835369|gb|CD975047.1|CD975047
EST:     ACCGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: A-CGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|32840727|gb|CD980408.1|CD980408
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|211157317|gb|FK993529.1|FK993529
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAG                         GAGCTGGCCGAGATAATGATTGGGAGAGTCCACAAT-GCCACAACATCA
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCA-AATTGCCACAACATCA
EST: gi|78026571|gb|DV494958.1|DV494958
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
EST: gi|32841497|gb|CD981178.1|CD981178
EST:     CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGCCTGCAG                         GAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT
genomic: CACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACT

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: 48 (upstream exon), 48 (downstream exon)
Score: 190

GGCACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 89

GGCACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 138

GGCACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 93

GGCACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatctta ... tctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCACGAGAGCTGGCTCATATTCTGATGAAGATTCTCAGAAGAAGTCTGCAGgtatatcttattgaatttgtattttgacttatttatattaatgtggttggcacgtgatgaattctttgcctatccctctgaacttctgatgcag

- - - AGAGCT
- - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - CTGCAG