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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATAGAGCCCTCAAGCTGCCAACTTTGCCAAAACCCCTGCTGGGAGTAATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaagatacaacactcatgttccttgttgcaaccttcattttaaaatcatttctgatacgtgacgccaaatccattagttgtcttgcctatctagatgattgatattgaagctttttttttttgcttcatcttacag

Basic information

species Zea mays
transcript GRMZM5G813909_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813909_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g45650.1 (Oryza sativa), 5'ss of exon 2
AGCATAGAGCCCTCAAGCTGCCAACTTTGCCAAAACCCCTGCTGGGAGTAATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaagatacaacactcatgttccttgttgcaaccttcattttaaaatcatttctgatacgtgacgccaaatccattagttgtcttgcctatctagatgattgatattgaagctttttttttttgcttcatcttacag
||||||||||||| ||| |||||||  |||||||||||||| | |||||||||||||  ||||||||||| ||||| |||||||||||||| || ||||||| |||| ||  |||  | ||||  ||     ||||||||||       | || |||  |  ||| ||    |   | |   |||  |   | ||  | |  |  | ||| |||    ||    ||| |||| ||| ||||||
AGCATAGAGCCCTTAAGTTGCCAACACTGCCAAAACCCCTGGTAGGAGTAATTAGTGGTGAAAAGTTTGAGCGCTCCAGAGCTTATAGCCTTGATAAAAGgtatgtgtaa--tactgctctcacctt-----ttgcaacctt-------acattattcattttac-tgcaatcg--ttctaaagtaattcagactgccaattttttggattttgtgtgttgacatttatgct-catgttacag
















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|211541246|gb|FL353980.1|FL353980
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTT-AATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211188255|gb|FL327236.1|FL327236
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|149101643|gb|EE187775.2|EE187775
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|71767568|gb|DR965505.1|DR965505
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211285085|gb|FL334458.1|FL334458
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTANAGCTTATAGCCTCGACAAAAG                         CTATTTTCCATTTTGTTCATGAGGCTGNGACTATTTTAATGGATACTACNA
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTT-CCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAA
EST: gi|29130241|gb|CB380945.1|CB380945
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211469576|gb|FL315154.1|FL315154
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|76293281|gb|DV032849.1|DV032849
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|71446633|gb|DR827683.1|DR827683
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211198069|gb|FL339164.1|FL339164
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCYTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCAYGAGGCTGTGACTATTTTAATGGA
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGA
EST: gi|211346647|gb|FL306883.1|FL306883
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATT
EST: gi|211337668|gb|FL335756.1|FL335756
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACCAA
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTAC-AA
EST: gi|71330641|gb|DR802092.1|DR802092
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211481369|gb|FL368104.1|FL368104
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACRAA
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTAC-AA
EST: gi|211477296|gb|FL319649.1|FL319649
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTKAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211414919|gb|FL346511.1|FL346511
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|78091217|gb|DV519591.1|DV519591
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211507618|gb|FL326181.1|FL326181
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211231531|gb|FL255915.1|FL255915
EST:     CTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: CTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211231534|gb|FL255918.1|FL255918
EST:     TTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: TTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211456968|gb|FL307879.1|FL307879
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|50322421|gb|CO517547.1|CO517547
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211023229|gb|FL319670.1|FL319670
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211274143|gb|FL330839.1|FL330839
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|78114998|gb|DV533386.1|DV533386
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|78113447|gb|DV531839.1|DV531839
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|50334362|gb|CO529488.1|CO529488
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211274560|gb|FL349473.1|FL349473
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|37424619|gb|CF650042.1|CF650042
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211203269|gb|FL344215.1|FL344215
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTANTGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211195422|gb|FL326474.1|FL326474
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|71436743|gb|DR817793.1|DR817793
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
EST: gi|211228866|gb|FL338409.1|FL338409
EST:     ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAG                         CTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT
genomic: ATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAAT

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: 46 (upstream exon), 49 (downstream exon)
Score: 122

AGCATAGAGCCCTCAAGCTGCCAACTTTGCCAAAACCCCTGCTGGGAGTAATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 66

AGCATAGAGCCCTCAAGCTGCCAACTTTGCCAAAACCCCTGCTGGGAGTAATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 79

AGCATAGAGCCCTCAAGCTGCCAACTTTGCCAAAACCCCTGCTGGGAGTAATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 102

AGCATAGAGCCCTCAAGCTGCCAACTTTGCCAAAACCCCTGCTGGGAGTAATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaa ... catcttacagCTATTTCCATTTTGTTCATGAGGCTGTGACTATTTTAATGGATACTACAATACTATACTATAGAGTTCTTCCCTGGTTTTGGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCATAGAGCCCTCAAGCTGCCAACTTTGCCAAAACCCCTGCTGGGAGTAATTAGTGACGAAAAGTTTGAACGCTCTAGAGCTTATAGCCTCGACAAAAGgtttgtgcaagatacaacactcatgttccttgttgcaaccttcattttaaaatcatttctgatacgtgacgccaaatccattagttgtcttgcctatctagatgattgatattgaagctttttttttttgcttcatcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT