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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGCCATCGTGCGGGCCGGGATGGCCGCCGCCGTGCAGCAGGAGCCGCGGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgcatgtcgtggcgccttgggcttgctgctggtcgtcagtatgcgtcgcgccgcgccatccatccaacactccattattattattattattgcccatgcag

Basic information

species Zea mays
transcript GRMZM2G405459_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G405459_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g14160.1 (Oryza sativa), 5'ss of exon 1
GCAGGCCATCGTGCGGGCCGGGATGGCCGCCGCCGTGCAGCAGGAGCCGCGGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaag-----catgcatgtcgtggcgccttg-----ggcttgc--tgctggtcgtcagtatgcgtcgcgccgcgccatccatccaacactccattattattattattattgcccatgcag--------
|||| |||||||| || | |  ||||| |||||||||||||| ||||| || ||||| ||||||||||||||||||||||||||||||||||||||| | |||||     |||   |  |  |    ||||     |||  ||  ||  ||   | || |||    |||    |  ||| | |  |   ||  |        ||  |   |   ||  |         
GCAGTCCATCGTGAGGTCGGCCATGGCGGCCGCCGTGCAGCAAGAGCCCCGCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagtacaccatagctagctagctagcttgagagtggccagccatggcggctctgagaatg-acggcggatggggatcgagctgatggtcgctcgccggcgttcatggcgattatatatgattgcag
















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|101391220|gb|EB817544.1|EB817544
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|74243836|gb|DT651750.1|DT651750
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|148990360|gb|EE031924.2|EE031924
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|211129110|gb|FL371870.1|FL371870
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|89758165|gb|DY687454.1|DY687454
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|148971747|gb|EE022480.2|EE022480
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|149077077|gb|EE165734.2|EE165734
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|211330555|gb|FL419743.1|FL419743
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|149109341|gb|EE190148.2|EE190148
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|211520759|gb|FL372667.1|FL372667
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|149011216|gb|EE042295.2|EE042295
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|18660431|gb|BM500858.1|BM500858
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGAGGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|149082902|gb|EE172134.2|EE172134
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|76011646|gb|DT938816.1|DT938816
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|149071215|gb|EE159609.2|EE159609
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|149106128|gb|EE291799.2|EE291799
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|149071959|gb|EE160346.2|EE160346
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|78104882|gb|DV523300.1|DV523300
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|91875137|gb|EB405094.1|EB405094
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|148934451|gb|EC878489.2|EC878489
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
EST: gi|71767442|gb|DR965379.1|DR965379
EST:     GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAG                         GGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG
genomic: GGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAG

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), 23 (downstream exon)
Score: 7

GCAGGCCATCGTGCGGGCCGGGATGGCCGCCGCCGTGCAGCAGGAGCCGCGGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAGAAGAACGCGGGGCCCAACGCCAACTCCCTGCGCGGCTTCGAGGTCATCG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 18

GCAGGCCATCGTGCGGGCCGGGATGGCCGCCGCCGTGCAGCAGGAGCCGCGGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAGAAGAACGCGGGGCCCAACGCCAACTCCCTGCGCGGCTTCGAGGTCATCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 46

GCAGGCCATCGTGCGGGCCGGGATGGCCGCCGCCGTGCAGCAGGAGCCGCGGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAGAAGAACGCGGGGCCCAACGCCAACTCCCTGCGCGGCTTCGAGGTCATCG


Block sizes: 47 (upstream exon), 36 (downstream exon)
Score: 8

GCAGGCCATCGTGCGGGCCGGGATGGCCGCCGCCGTGCAGCAGGAGCCGCGGATGGGGGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGgtaagcatgc ... gcccatgcagGGGTGCGACGCGTCCGTGCTCCTCGACGACTCGCCGACGCTGACGGGGGAGAAGAACGCGGGGCCCAACGCCAACTCCCTGCGCGGCTTCGAGGTCATCG