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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTCTCACCATCAGGACCGCCGTCTCGACGGCCGTGCTGCTGGAGCCCCGCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatcagtcgtctcaatctaacagagacgacagatagtgagtgagtgagtgagtgaccatggctctgcgctgtgtatatgcatgcacctattatatgtacggcag

Basic information

species Zea mays
transcript GRMZM2G020523_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020523_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g32050.1 (Oryza sativa), 5'ss of exon 1
CCTTCTCACCATCAGGACCGCCGTCTCGACGGCCGTGCTGCTGGAGCCCCGCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatcagtcgtct--caatctaacagagacgacagatagtgagtgagtgagtgagtgaccatggctctgcgctgtgtatatgcatgcacctattatatgtacggcag
 || |||||||||||||||| ||| ||| |||| |||||||| || ||||||||||| |||||||| ||||||||||||||||||||||| ||||| |||| || | | |  ||   |   |||    |     |  | |  |      ||  |  || ||   | | | |||    ||   ||  |||||||  | | || |         
GCTGCTCACCATCAGGACCGTCGTGTCGGCGGCGGTGCTGCTCGACCCCCGCATGGGCGCCTCCCTCCTCCGCCTCCACTTCCACGACTGCTTCGTCCAGgcaattaagctatcccttgttaattctccttcccctccggccaccagtcgatcgtctg-gtcgtcgtcgatctcgattg---attggcatgcatgtctcatgtag-------
















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|78110954|gb|DV529352.1|DV529352
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|50330214|gb|CO525340.1|CO525340
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|93014704|gb|EB640224.1|EB640224
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|71430666|gb|DR811716.1|DR811716
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|149090376|gb|EE179684.2|EE179684
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|211277208|gb|FL063663.1|FL063663
EST:     GCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|211275409|gb|FL063662.1|FL063662
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|78084057|gb|DV512450.1|DV512450
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|76935157|gb|DV174204.1|DV174204
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|91048009|gb|EB158427.1|EB158427
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|89758624|gb|DY687739.1|DY687739
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|38687661|gb|CK144692.1|CK144692
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|76289009|gb|DV028577.1|DV028577
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|50328204|gb|CO523330.1|CO523330
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|91048790|gb|EB159208.1|EB159208
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|211275408|gb|FL063661.1|FL063661
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|76280543|gb|DV020111.1|DV020111
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
EST: gi|76285538|gb|DV025106.1|DV025106
EST:     GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAG                         GGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG
genomic: GCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAG

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 2 RNA-Seq libraries.


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 16

CCTTCTCACCATCAGGACCGCCGTCTCGACGGCCGTGCTGCTGGAGCCCCGCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAGAAGGGGGCGGGGCCGAACGCGGGGTCGCTCCGGGGCTTCGACGTGATCG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 10

CCTTCTCACCATCAGGACCGCCGTCTCGACGGCCGTGCTGCTGGAGCCCCGCATGGGGGCCTCCCTTCTCCGCCTCCACTTCCACGACTGTTTCGTGCAGgtaagtcatc ... tgtacggcagGGTTGCGACGCGTCGGTGCTGCTAGACGACACGGCGAGCTTCACCGGCGAGAAGGGGGCGGGGCCGAACGCGGGGTCGCTCCGGGGCTTCGACGTGATCG




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