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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taactatgaatatatcaatttatgaatagtgtaaaagcactttttcctaacaatatgttatttcccagactactgcccctcacttttaactttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCTCTCAATGGTGTTGGTCTTTGTCCTGCTAGTAGATCACTTAGCACCCATG

Basic information

species Zea mays
transcript GRMZM5G877597_T02
intron # 3
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|91054928|gb|EB165346.1|EB165346
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|78090489|gb|DV518863.1|DV518863
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|91054929|gb|EB165347.1|EB165347
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|94472958|gb|EB701916.1|EB701916
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|71431610|gb|DR812660.1|DR812660
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|78084750|gb|DV513143.1|DV513143
EST:     AAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: AAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|71311298|gb|DR791964.1|DR791964
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|74246237|gb|DT654151.1|DT654151
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT
EST: gi|88748255|gb|DY532396.1|DY532396
EST:     CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAG                         GCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACGGCCTGCTCATTCT
genomic: CAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCT

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), 46 (downstream exon)
Score: 25

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCTCTCAATGGTGTTGGTCTTTGTCCTGCTAGTAGATCACTTAGCACCCATG


Block sizes: 41 (upstream exon), 44 (downstream exon)
Score: 18

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCTCTCAATGGTGTTGGTCTTTGTCCTGCTAGTAGATCACTTAGCACCCATG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 24

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCTCTCAATGGTGTTGGTCTTTGTCCTGCTAGTAGATCACTTAGCACCCATG


Block sizes: 45 (upstream exon), 39 (downstream exon)
Score: 22

GTCTCTTAAACATGAAGATGCGGAGAACATAGGTTATGTGATACCGACTCCAGTTATTACACATTTCATTGAGGACTACAAAAATCTAGAGAATACACAGgtaatatgct ... tttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCTCTCAATGGTGTTGGTCTTTGTCCTGCTAGTAGATCACTTAGCACCCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctaacaatatgttatttcccagactactgcccctcacttttaactttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCTCTCAATGGTGTTGGTCTTTGTCCTGCTAGTAGATCACTTAGCACCCATG
                              cccctcacttttaact  CT-rich tract
                                      ttttaactttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taactatgaatatatcaatttatgaatagtgtaaaagcactttttcctaacaatatgttatttcccagactactgcccctcacttttaactttctttcagGCTGCAATTGAGTACATTCATTCTTTATCAAGGGCACAGCCTGCTCATTCTCTCAATGGTGTTGGTCTTTGTCCTGCTAGTAGATCACTTAGCACCCATG

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