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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttcatcttttctctatgctttctagctaatctcgacttttatgtgtctgtcttggctctgccttacagtttgtatttcatgctggtag

Basic information

species Zea mays
transcript GRMZM2G701689_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G701689_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g41230.2 (Oryza sativa), 5'ss of exon 2
ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttcatcttttctctatgctttctagctaatctcgacttttatgtgtctgtcttggctctgccttacagtttgtatttc-atgctggtag-
||||||| || ||||||||||||||||| ||||| |||||||| || |||||||||||||||||||| |||||  |||||| | ||||| |||  |||||||  ||||    || || ||||    ||  |  |||| ||  | |||  |  | |  |||  || |  || |||   ||||| || ||  |      
ATAATGTTCAACTATTCAAGTCATCAGACTTGGCTCCTGTTTCCTCAATCTTTGCCTCACCACATGTCAATCCTGCAAAGGAATCTAAACTTCCAATCAGgtaaatttatg-ctattttctag---ttgaatgtaatttcatccttttaggctttagctta-ctatatct-aca---tgtatctccatattaaccag
















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|211366534|gb|FL297817.1|FL297817
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|87152637|gb|DY397426.1|DY397426
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211513604|gb|FL043440.1|FL043440
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTTAGCAGTGTCA
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCT-AGCAGTGTCA
EST: gi|211366529|gb|FL297812.1|FL297812
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|19272496|gb|BM888752.1|BM888752
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366525|gb|FL297808.1|FL297808
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|87152122|gb|DY396911.1|DY396911
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366538|gb|FL297821.1|FL297821
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|19437165|gb|BM953575.1|BM953575
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366527|gb|FL297810.1|FL297810
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366530|gb|FL297813.1|FL297813
EST:     TTGCCTCACCACATGTTAATCCAACAAGGGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGC-CTCCACCTAGCAGTGTCA
genomic: TTGCCTCACCACATGTTAATCCAACAAAGGG-AACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTC-ACCTAGCAGTGTCA
EST: gi|211366524|gb|FL297807.1|FL297807
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|71312702|gb|DR792875.1|DR792875
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366536|gb|FL297819.1|FL297819
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366537|gb|FL297820.1|FL297820
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGGGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211369184|gb|FL297822.1|FL297822
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211363879|gb|FL297806.1|FL297806
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211363877|gb|FL297804.1|FL297804
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211404142|gb|FL328727.1|FL328727
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366531|gb|FL297814.1|FL297814
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366532|gb|FL297815.1|FL297815
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|211366526|gb|FL297809.1|FL297809
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|22491113|gb|BU051036.1|BU051036
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
EST: gi|22490856|gb|BU050779.1|BU050779
EST:     TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAG                         GGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG
genomic: TTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAG

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), 48 (downstream exon)
Score: 980

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 633

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 820

ATAATGTGCAGCTATTCAAGTCATCAGATTTGGCACCTGTTTCTTCGATCTTTGCCTCACCACATGTTAATCCAACAAAGGGAACTAAAGTTCTGATCAGgtttattttc ... atgctggtagGGACGAATCTGTTCAGCTTCCTCATGAATTGCACTCACCTAGCAGTGTCAGAACTCGGATAGGCACCTCAGGCTCTTTTAGAATGATCAGATGCAAAGAC