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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggctctcgaagtaaactcttttgtgggcattaagctcttgaattaccagcaacaacaagctttccaacagtctgatttattattctttgatttgatcatatgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTA

Basic information

species Zea mays
transcript GRMZM2G104294_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104294_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 3'ss of exon 13
gtaggctct-----cgaagta-aactct-tttgtgggcattaagctcttgaattaccagcaacaacaa-------gctttc--caacagtctgatttattattctttgatttgatcatatgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTA
||  | |       | || || |||||| | | |    ||     | ||| ||| || ||||  ||||       | || |  || |||| ||| |||||  || |  |    |  || | ||| | ||||  |||| ||    |||||||| ||||| || |||||||| || || | |||||||||||||||||| ||||| ||||| || ||  ||||||| ||||
gtgagtttcttgtacaaattataactctctctctatatatctctatattgcattgcctgcaatgacaatgagaaggtttcctacagcagtttgacttattcctcctccac---aatatctactttgtagAACGCAATCCCATCAGAATATAGTGAAGAGTGTAGCTGGGCACCAATTTATGTGAGGCAGTCAAATTTTAAGTTGCCTGCAGATCCGACCACTCCAATTA
















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|20506752|gb|BQ279326.1|BQ279326
EST:     CTTCACCAACAGGAAGGGTCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATA
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATA
EST: gi|32928790|gb|CF033602.1|CF033602
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|194716812|gb|FK933971.1|FK933971
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32921358|gb|CF026170.1|CF026170
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32832538|gb|CD972216.1|CD972216
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32929828|gb|CF034640.1|CF034640
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|67024128|gb|CO452877.1|CO452877
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32921381|gb|CF026193.1|CF026193
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|211465905|gb|FL134197.1|FL134197
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32835489|gb|CD975167.1|CD975167
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32928791|gb|CF033603.1|CF033603
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGACTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32929541|gb|CF034353.1|CF034353
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32835138|gb|CD974816.1|CD974816
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTNTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|13316177|gb|BG410624.1|BG410624
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGCTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATCTTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|61119293|gb|DN560254.1|DN560254
EST:     CTTCACCAACAGGAAGGGTCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|6828127|gb|AW331770.1|AW331770
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTCGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCT
EST: gi|32921780|gb|CF026592.1|CF026592
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
EST: gi|32920698|gb|CF025510.1|CF025510
EST:     CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAG                         AATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT
genomic: CTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTT

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: 631

GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 724

GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 819

GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1117

GATGGCTCCCTCCAGAATTCATGTAACATGTGCATTAGTTTATGGGCCTTCACCAACAGGAAGGATCCACCAAGGAGTTTGTTCAACATGGATGAAGgtaggctctc ... tgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagctttccaacagtctgatttattattctttgatttgatcatatgcttggcagAATACAATTCCTCTGGAATATAGCGAAGAATGCAGCTGGGCTCCCATATTTGTGAGGCAGTCAAATTTCAAGTTACCTGCTGACCCATCCACTCCGATTA
                   atttattattctttga  TA-rich tract