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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgattgtttgaagatccttttgttgtgcatgcattctcttttaccctcgattgggtatagatcaaactaactattgtggtatgctcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATTCGATGCCCAGTCGGAATATTTATAGGGTTTTCATTACAAGTAAATATGT

Basic information

species Zea mays
transcript GRMZM2G558539_T02
intron # 11
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|60339589|gb|DN206562.1|DN206562
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|60358480|gb|DN225453.1|DN225453
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|86471474|gb|DY237844.1|DY237844
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATTTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|5936814|gb|AW060082.1|AW060082
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|60354187|gb|DN221160.1|DN221160
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|84908799|gb|DW404677.1|DW404677
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAGATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|76925222|gb|DV170325.1|DV170325
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTTTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATTTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|78179234|gb|DV549607.1|DV549607
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCAGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|60398906|gb|DN231722.1|DN231722
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|71300395|gb|DR786266.1|DR786266
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|60340147|gb|DN207120.1|DN207120
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|86474502|gb|DY240872.1|DY240872
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTTTGATAAAATAAACAG                         GACGTCCTCCATCAAATTTGCCAGCTAATTATTATTTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|71772068|gb|DR970005.1|DR970005
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|8577220|gb|BE129857.1|BE129857
EST:     CCATTGATATGCTGTTGAAAGATGCTGATTCCTCAT-ATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: CCATTGATATGCTGTTGAAAGATGCTGATTCCTC-TGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|32932367|gb|CF037179.1|CF037179
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGACACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|211347566|gb|FL462326.1|FL462326
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|32832466|gb|CD972144.1|CD972144
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|60354933|gb|DN221906.1|DN221906
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|110944775|gb|EE164932.1|EE164932
EST:     CCCATTGATATGCTGTTGAAAGATGCTGATTCCTTTGATAAAATAAACAG                         GACGTCCTCCATCAAATTTGCCAGCTAATTATTATTTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|71329626|gb|DR801542.1|DR801542
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|32833562|gb|CD973240.1|CD973240
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|211119819|gb|FL462976.1|FL462976
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCAGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|93011741|gb|EB637261.1|EB637261
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTTTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATTTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|93282521|gb|EB674785.1|EB674785
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|71321373|gb|DR797399.1|DR797399
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|71332095|gb|DR802954.1|DR802954
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATTTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
EST: gi|32833782|gb|CD973460.1|CD973460
EST:     ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAG                         GACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT
genomic: ACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATT

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: 111

GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATTCGATGCCCAGTCGGAATATTTATAGGGTTTTCATTACAAGTAAATATGT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 218

GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATTCGATGCCCAGTCGGAATATTTATAGGGTTTTCATTACAAGTAAATATGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 184

GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATTCGATGCCCAGTCGGAATATTTATAGGGTTTTCATTACAAGTAAATATGT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 157

GGATTGCAACTGGCAATAGAATCAGGGAATTGTGGCAAGGACACCATTGATATGCTGTTGAAAGATGCTGATTCCTCTGATAAAATAAACAGgtttgattgt ... tcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATTCGATGCCCAGTCGGAATATTTATAGGGTTTTCATTACAAGTAAATATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaccctcgattgggtatagatcaaactaactattgtggtatgctcatttgcagGACGTCCTCCATCAAATCTGCCAGCTAATTATTATCTGGTCGATACTGATTCGATGCCCAGTCGGAATATTTATAGGGTTTTCATTACAAGTAAATATGT
                         aactaac  putative branch site (score: 157)
                                            ctcattt  putative PPT
                            taactatt  TA-rich tract