Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctggttttctggacaaagatcgcatatttagtcaattacgtctactcatcctttttcccttcatttcatttgattgaatgatacataaccattcacgtcttttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG

Basic information

species Zea mays
transcript GRMZM2G018447_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018447_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g44000.1 (Oryza sativa), 3'ss of exon 3
----gtctggttttctggacaaa--gatcgcatatttagtcaattacgtctactcatcctttttcccttcat---ttcatttgattgaat---gatacataaccattcacgtcttttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG
    |  |  |||||   ||| |    |  |  || |||  |  |     || || |    ||||   ||||   |||  |  |||  ||   | | || |   ||| |  |||||   |||||||||||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| ||||
gtgagctttcttttcacaacagattactttctcatatagaaacctttaattaatcctttcgtttcttctcatctgttccctgcattcgatttggttgcaaactaatttaactctttca-ttccagGTCATTTTTCTCAACCCGGCGCCGATGCATCCACACATTTACAGCAACGGGCACATCTGTTTAG
















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|211424407|gb|FL084942.1|FL084942
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|32868298|gb|CF007980.1|CF007980
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424414|gb|FL084949.1|FL084949
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424415|gb|FL084950.1|FL084950
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|76018971|gb|DT946141.1|DT946141
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424413|gb|FL084948.1|FL084948
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCNATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|32869440|gb|CF009122.1|CF009122
EST:     ACCATTTTTTGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424416|gb|FL084951.1|FL084951
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421813|gb|FL084940.1|FL084940
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|32856121|gb|CD995802.1|CD995802
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421814|gb|FL084941.1|FL084941
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|89756005|gb|DY686208.1|DY686208
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421803|gb|FL084930.1|FL084930
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCTAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|67016859|gb|CO445608.1|CO445608
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|18166490|gb|BM336329.1|BM336329
EST:     AGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: AGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|89246821|gb|DY618608.1|DY618608
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424417|gb|FL084952.1|FL084952
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421809|gb|FL084936.1|FL084936
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|16920438|gb|BM074657.1|BM074657
EST:     ACCAGTTGCAGGTTGACTTCCGTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|76288121|gb|DV027689.1|DV027689
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|60394784|gb|DN227654.1|DN227654
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|32935782|gb|CF040594.1|CF040594
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|76018970|gb|DT946140.1|DT946140
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|18172273|gb|BM347661.1|BM347661
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424418|gb|FL084953.1|FL084953
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|116821688|gb|EC865015.1|EC865015
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCAACTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|29947193|gb|CB816528.1|CB816528
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|17929384|gb|BM266344.1|BM266344
EST:     ACCAGTTGCAGGTTGACTTCCNTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|76288120|gb|DV027688.1|DV027688
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421805|gb|FL084932.1|FL084932
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421806|gb|FL084933.1|FL084933
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421802|gb|FL084929.1|FL084929
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|18163588|gb|BM333427.1|BM333427
EST:     AGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: AGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211424411|gb|FL084946.1|FL084946
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|211421808|gb|FL084935.1|FL084935
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
EST: gi|18169036|gb|BM338876.1|BM338876
EST:     ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAG                         GTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG
genomic: ACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGG

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: 253

GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 601

GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 737

GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 395

GGTAATTGAGGTCACTGGAGCGGCGGGCACCCTTTACGCCGGCGAGACCTACCAGTTGCAGGTTGACTTCCCTGAGCATTATCCTATGGAGGCACCTCAGgtctggtttt ... ttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttcatttcatttgattgaatgatacataaccattcacgtcttttgcttccagGTCATTTTTCTCAATCCAGCGCCAATGCATCCACACATCTACAGCAACGGGCACATCTGCTTAG
                          acataac  putative branch site (score: 395)
                                       cgtcttttgcttcc  putative PPT
      atttcattt  TA-rich tract