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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGCCAGTACGGTCCAAAGAGCAGGTGAGGGAGCTCGTCCCCATCGACCTTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccgtatccctacatttgtagctacggaaagctcggttccattgagttacttgtcgtagtgctttgggattactaagggggtgtttgaatccac...

Basic information

species Zea mays
transcript GRMZM2G024738_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024738_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g43390.1 (Oryza sativa), 5'ss of exon 2
ATCGCCAGTACGGTCCAAAGAGCAGGTGAGGGAGCTCGTCCCCATCGACCTTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccgtatccctacatttgtagctacggaaagctcggttccattga-----gttacttgtcgtagtgctttgggattactaagggggtgtttgaatccac
 || || ||  ||||| | ||||||||||||||||||  |||||| ||| | || | ||||| ||||||||| ||||| || |||||||| || | ||||||||||| |      | |  ||||| |    | ||| | |  |||  || |     |||   ||       | || |||  |  | | |   || |  |||  | 
GTCTCCCGTGAGGTCCGAGGAGCAGGTGAGGGAGCTCACCCCCATTGACTTCGAGAAGCTCCGGTTCGTCGGTGAGTCGCTCAAGATTCTACGCACTGAGgtaatgcgcag----ccatttttgtggtatggaaaaccccctttctgttaaaatttgttgtatgaaactcggtttgggggctcatgatgaattggtacaatgta-
















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|50334939|gb|CO530065.1|CO530065
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGNAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|87152167|gb|DY396956.1|DY396956
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|71329891|gb|DR801664.1|DR801664
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|78122182|gb|DV540566.1|DV540566
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|71418375|gb|DR804419.1|DR804419
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|76928473|gb|DV171639.1|DV171639
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|74241023|gb|DT648937.1|DT648937
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|32920184|gb|CF024996.1|CF024996
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|149048891|gb|EE048391.2|EE048391
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|76292919|gb|DV032487.1|DV032487
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|60352724|gb|DN219697.1|DN219697
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTGAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|32921233|gb|CF026045.1|CF026045
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|74243528|gb|DT651442.1|DT651442
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|50335320|gb|CO530446.1|CO530446
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|148958901|gb|EE010466.2|EE010466
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|211179950|gb|FL166416.1|FL166416
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTGAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|91049477|gb|EB159895.1|EB159895
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|32921133|gb|CF025945.1|CF025945
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|148991743|gb|EE033314.2|EE033314
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|31350291|gb|CD434648.1|CD434648
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|21843215|gb|BQ703796.1|BQ703796
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|71447413|gb|DR828463.1|DR828463
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|93012244|gb|EB637764.1|EB637764
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|32921178|gb|CF025990.1|CF025990
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
EST: gi|76280664|gb|DV020232.1|DV020232
EST:     TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAG                         ATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT
genomic: TTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATT

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: 47 (upstream exon), 48 (downstream exon)
Score: 57

ATCGCCAGTACGGTCCAAAGAGCAGGTGAGGGAGCTCGTCCCCATCGACCTTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATTGCAACTTACATTGTTGAAGGGGGGATGACCAATACGTACACAAATATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

ATCGCCAGTACGGTCCAAAGAGCAGGTGAGGGAGCTCGTCCCCATCGACCTTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATTGCAACTTACATTGTTGAAGGGGGGATGACCAATACGTACACAAATATAA


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 30

ATCGCCAGTACGGTCCAAAGAGCAGGTGAGGGAGCTCGTCCCCATCGACCTTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATTGCAACTTACATTGTTGAAGGGGGGATGACCAATACGTACACAAATATAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 101

ATCGCCAGTACGGTCCAAAGAGCAGGTGAGGGAGCTCGTCCCCATCGACCTTGATATGCTCCAGTTCGTCGGGGAGTCACTAAAGATTCTGCGAAATGAGgtaatgcccg ... tatcctctagATTGATGGAAAAGCTGCTTTGCTAGGATTTGTGGGGGCCCCATGGACAATTGCAACTTACATTGTTGAAGGGGGGATGACCAATACGTACACAAATATAA