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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGATCTACTTGGTTCTGTGGATGAGATATTATATGATATTTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttgcagtgtatgttaatagaatgaacatttaactttactgtttaaacattctactaaatctttgtggctgtttcaccgtgcag

Basic information

species Zea mays
transcript GRMZM2G435373_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G435373_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 11
AATTGATCTACTTGGTTCTGTGGATGAGATATTATATGATATTTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttgcagtgtatg-ttaatagaatgaacatttaactttactgtttaaacattctactaaatctttgtggctgtttcaccgtgcag
||||||||||||||||   || |||||| |||| | |||||| ||||| ||||| ||||| |||||||||||||||||||||||||| |||||| |||| ||||| |||||| | | || ||  |  ||||| |||| |  || | ||| || ||    |   | || ||| |||      | || |||||
AATTGATCTACTTGGTCAAGTAGATGAGCTATTTTTTGATATCTATGATAGATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttgcaatatctgatttttgaaatgagcattaagtttgattgtctagac----tgtaacatatttctggtccacactccctgcag

upper sequence: GRMZM2G435373_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g34540.1 (Oryza sativa), 5'ss of exon 11
AATTGATCTACTTGGTTCTGTGGATGAGATATTATATGATATTTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttgcagtgtatgttaatagaat-gaacatttaactttactg--tttaaacattctacta--aatctttgtggctgtt--tcaccgtgcag
 |||||||||||||||   || |||||| |||| | |||||| ||||| ||||||||||| |||||||| |||||||||||||| || |||||| |||| ||||| | | | ||||||| |  |  | | ||||||| |  ||   ||  ||  |  ||  || ||  ||  | | ||| ||||  || |  |||||
GATTGATCTACTTGGTCAAGTAGATGAGCTATTCTTTGATATCTATGATAGATATGAACCCGTGAATGAGCCATCTCTTGATAACTGTTTTGTCTCAACTgtaagttctacggtgtatgattttgcacttgaacattaagtttggttgtgttggagtataatagtataaacatctctggttgttattctctctgcag
















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|5597098|gb|AI891301.1|AI891301
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|5901102|gb|AW042202.1|AW042202
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|24934285|gb|CA452503.1|CA452503
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|213167548|gb|FM181807.1|FM181807
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|37401104|gb|CF637915.1|CF637915
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|67031426|gb|CO460175.1|CO460175
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|5895890|gb|AW037136.1|AW037136
EST:     AACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: AACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|37401085|gb|CF637905.1|CF637905
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|33093438|gb|CF053432.1|CF053432
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|60396805|gb|DN229633.1|DN229633
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|5871395|gb|AW017866.1|AW017866
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCCCAACG                         AGCTATGACGCCCCCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|33095264|gb|CF055258.1|CF055258
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|6828046|gb|AW331689.1|AW331689
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|60398565|gb|DN231381.1|DN231381
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|5901209|gb|AW042309.1|AW042309
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTTACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|33102234|gb|CF062194.1|CF062194
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|211493510|gb|FL163238.1|FL163238
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|33095120|gb|CF055114.1|CF055114
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|37384015|gb|CF629050.1|CF629050
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|31612098|gb|CD568720.1|CD568720
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|67021306|gb|CO450055.1|CO450055
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|5525493|gb|AI861386.1|AI861386
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACCCATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|33091488|gb|CF051482.1|CF051482
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|32933839|gb|CF038651.1|CF038651
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|60359326|gb|DN226299.1|DN226299
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|30087662|gb|CB885868.1|CB885868
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|32919393|gb|CF024205.1|CF024205
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|113704014|gb|EE681518.1|EE681518
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|5915143|gb|AW052784.1|AW052784
EST:     GATATGAACCAGGGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|33093030|gb|CF053024.1|CF053024
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|78021844|gb|DV490231.1|DV490231
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|60355746|gb|DN222719.1|DN222719
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|32930298|gb|CF035110.1|CF035110
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGACACAACG                         AGCTATGACGCGACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|149098466|gb|EE184445.2|EE184445
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|67014412|gb|CO443161.1|CO443161
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
EST: gi|211493511|gb|FL163239.1|FL163239
EST:     GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACG                         AGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC
genomic: GATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAAC

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: 157

AATTGATCTACTTGGTTCTGTGGATGAGATATTATATGATATTTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAACATGTATACAATGATCACTGGAAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 64

AATTGATCTACTTGGTTCTGTGGATGAGATATTATATGATATTTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAACATGTATACAATGATCACTGGAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 44

AATTGATCTACTTGGTTCTGTGGATGAGATATTATATGATATTTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAACATGTATACAATGATCACTGGAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

AATTGATCTACTTGGTTCTGTGGATGAGATATTATATGATATTTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttg ... caccgtgcagAGCTATGACGCCACCACACATTTTGAGACAACTGTAACAGATGTCCTGAACATGTATACAATGATCACTGGAAAG