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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaagatatgacgtgtgcacctttttcatcgttaaatattgcacgatgtattctttcttatggaattctgcatttccacttccatacctaattg...

Basic information

species Zea mays
transcript GRMZM2G068586_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068586_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g48370.1 (Oryza sativa), 5'ss of exon 2
CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagt----------agaagatatgacgtgtgcacctttttcatcgttaaatattgcacgatgtattctttcttatggaattctgcatttccacttccatacctaattg
|||||||||||||||   |||||||| || || || ||| |||||||||| |||||||| ||||||||||||||||| || |||| | ||||||          |   ||| |||  || | || |  || |   | |  ||||    | || ||   | |       | | ||  | |   | || |          
CCAGGGCCAAGGGAGTTCCCAATGCAATGTTTCATTAAGCGGAATAAGAAGAACTCTACGTTCTACCTCTACCTTGGTTTGACAAATGgtaagtgtatgactgtacgtgatgtgatatgagaacttccttgactctcatttattttgtgctgcatatgtgcaggcatcaatttgattatgtgcatcta----------
















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|26456630|gb|CA828213.1|CA828213
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|211227913|gb|FL059245.1|FL059245
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGT
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTG-TGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGT
EST: gi|71772807|gb|DR970732.1|DR970732
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCT
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCT
EST: gi|148950368|gb|EC895931.2|EC895931
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|211227911|gb|FL059243.1|FL059243
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTT-CTCATGGCTGCTAGAAGATT-AGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|211227905|gb|FL059237.1|FL059237
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTTAGGCGT
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTT-AGGCGT
EST: gi|78078970|gb|DV507382.1|DV507382
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|149111829|gb|EE190984.2|EE190984
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|71310923|gb|DR791764.1|DR791764
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|76914172|gb|DV165433.1|DV165433
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|20803223|gb|BQ294273.1|BQ294273
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|211227912|gb|FL059244.1|FL059244
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGT
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGT
EST: gi|67022110|gb|CO450859.1|CO450859
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGCT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTG
EST: gi|211227918|gb|FL059250.1|FL059250
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGAT
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGAT
EST: gi|211229972|gb|FL059251.1|FL059251
EST:     GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT                         CACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAA
genomic: GAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAA

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: 202

CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTGGTCCCCATACCGAGTACATTATATCTCTTGATGCAGAAGACTTATCACA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 162

CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTGGTCCCCATACCGAGTACATTATATCTCTTGATGCAGAAGACTTATCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTGGTCCCCATACCGAGTACATTATATCTCTTGATGCAGAAGACTTATCACA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 116

CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaa ... catctgacagCACCTGTGGATAAAGGGAAGTTTCTCATGGCTGCTAGAAGATTTAGGCGTGGTCCCCATACCGAGTACATTATATCTCTTGATGCAGAAGACTTATCACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTTgtaagtagaagatatgacgtgtgcacctttttcatcgttaaatattgcacgatgtattctttcttatggaattctgcatttccacttccatacctaattg

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