Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgggctgcccggccccttcggttctccagtctcttccggagttcgctgccgcccccgagcattagtctaatcttgggttcgattccgggccactctgcctcacttcgtcctccctctcctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAAGACCTCGAGCGCGCCGGAGGCGTCGACAGCGGGGCCCTCACCGTCGATG

Basic information

species Zea mays
transcript GRMZM2G177912_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177912_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 3'ss of exon 2
gtatgtgtgggctgcccggccccttcggttctccagtctcttccggagttcgctgccgcccccgagcattagtctaatcttgggttcgattccgggccactctgcctcacttcgtcctccctctcctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAAGACCTCGAGCGCGCCGGAGGCGTCGACAGCGGGGCCCTCACCGTCGATG
                                            | |   |    |  | |     |   |     ||||     | |   ||  ||      ||    | |  |  |||  |  || |  ||||| ||||| ||| ||||||| || |||||||||||||||||||||||||| || || ||||||||||| || ||||| || ||||| |||||||| || |
--------------------------------------------gtaacccatctcttctcttctccccgatctcgatctcc--cttgccccccagctctcacgcgattcctattattcctgccgctgctgcagTCCAACGTCTTCATCGAGGGGGTCTCGCACAAGATCCGGAGGCAGATCGAGGAGCTAGAGCGCGCCGGGGGTGTCGAGAGTGGGGCTCTCACCGTTGACG
















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|211359331|gb|FL325567.1|FL325567
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|71327563|gb|DR800390.1|DR800390
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|9953349|gb|BE639932.1|BE639932
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|8367294|gb|BE050239.1|BE050239
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211542143|gb|FL390828.1|FL390828
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTT
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTT
EST: gi|78120131|gb|DV538515.1|DV538515
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211218538|gb|FL338330.1|FL338330
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGS-ATGAYCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAG-CAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211114226|gb|FL350275.1|FL350275
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGAWCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211267792|gb|FL344631.1|FL344631
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211217973|gb|FL307283.1|FL307283
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|67016433|gb|CO445182.1|CO445182
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|71303539|gb|DR787880.1|DR787880
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|67042528|gb|CO468783.1|CO468783
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGAAGGCAGATCGAG
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211362192|gb|FL333555.1|FL333555
EST:     GCGTCGGCACCCTCGACTCCCTCSTYGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|149104624|gb|EE290073.2|EE290073
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211316704|gb|FL359227.1|FL359227
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTTGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|148969238|gb|EE019992.2|EE019992
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211105804|gb|FL320712.1|FL320712
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211283545|gb|FL347777.1|FL347777
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211064773|gb|FL350726.1|FL350726
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211460898|gb|FL364621.1|FL364621
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|76288290|gb|DV027858.1|DV027858
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211078718|gb|FL360383.1|FL360383
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCAAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211414492|gb|FL334083.1|FL334083
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211381249|gb|FL356117.1|FL356117
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
EST: gi|211467481|gb|FL327941.1|FL327941
EST:     GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAG                         TCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA
genomic: GCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAA

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), 49 (downstream exon)
Score: 90

TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAAGACCTCGAGCGCGCCGGAGGCGTCGACAGCGGGGCCCTCACCGTCGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 111

TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAAGACCTCGAGCGCGCCGGAGGCGTCGACAGCGGGGCCCTCACCGTCGATG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 94

TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAAGACCTCGAGCGCGCCGGAGGCGTCGACAGCGGGGCCCTCACCGTCGATG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 100

TTCAACGTCCCGGACCTCCGCGTCGGCACCCTCGACTCCCTCCTCGCGCTCAGCGATGACCTCGTCAAGgtatgtgtgg ... cctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAAGACCTCGAGCGCGCCGGAGGCGTCGACAGCGGGGCCCTCACCGTCGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggttcgattccgggccactctgcctcacttcgtcctccctctcctccgccagTCAAACGTGTTCGTCGAGGGCGTTTCGCACAAGATCCGGAGGCAGATCGAAGACCTCGAGCGCGCCGGAGGCGTCGACAGCGGGGCCCTCACCGTCGATG
                        gcctcac  putative branch site (score: 100)
                 ccactctgcctcactt  CT-rich tract