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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCGGAGTTTTGGATCCCATGAGGACGAAGACAGGAGTTCAGGGAACCCTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggctgaaattgtcttggttggctataacgtaacatcctgagcttcaatgcttccttgatcagagcttgataggcattagctgttgtgaaacat...

Basic information

species Oryza sativa
transcript LOC_Os03g15900.2
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15900.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G012319_T01 (Zea mays), 5'ss of exon 23
TGGTCGGAGTTTTGGATCCCATGAGGACGAAGACAGGAGTTCAGGGAACCCTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggctgaaattgtcttggttggctataacgtaacatcctgagcttcaatgcttccttgatcagagcttgataggcattagctgttgtgaaacat----
 || || ||||| |||||||| ||||| ||||| | |||||| || |||||||| |||||||||||  ||||||||||||||||||| || |||||||||||| |  ||  | |||  | || ||||  | |    |||  ||||||  |   || ||||| || |||||| ||||| |  | |    ||| |||||  |    
AGGACGAAGTTTCGGATCCCACGAGGATGAAGATAAGAGTTCTGGTAACCCTCAGTCTGGGAAAGCTTTGTATGACTTCACAGCAGGCGGTGATGATGAGgtacgcgggtagtaatcctttttgttgtttgtcttataaattcctgaagt--gatacttccatgttcagagtttgatgg--aatgttggttctgaaatcttttt

upper sequence: LOC_Os03g15900.2 (Oryza sativa), 5'ss of exon 21
lower sequence: AT2G07360.1 (Arabidopsis thaliana), 5'ss of exon 25
TGGTCGGAGTTTTGGATCCCATGAGGACGAAGACAGGAGTTCAGGGAACCCTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggctgaaattgtcttggttggctataacgtaacatcctgagcttcaatgcttccttgatcagagcttgataggcat-tagctgttgtgaaacat
|  ||| |||| || |||  |||| || |||   ||||  ||        |   || ||| | ||| || ||||||||||||||||| || ||||||||||||   ||  ||   |||||||   |   | ||   |   || | |      |||      ||   || |  || | |  | | | | | |  || |    
TTCTCGAAGTTATGAATCAGATGATGAAGAACCTAGGAAATCTACTGGTACAAGATTTGGAACAGCGCTCTATGACTTCACAGCAGGAGGAGATGATGAGgta---agcttgcttttgtcttttattcatttagttttgtatacggttgaaaaatatgatattatgcaaacgttaaaacacgtatgggtatgttgcag---
















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|29616695|gb|CB621707.1|CB621707
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|29616694|gb|CB621706.1|CB621706
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|29626872|gb|CB631883.1|CB631883
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|29672533|gb|CB668808.1|CB668808
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|86478908|gb|CI121541.1|CI121541
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGCGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|58674583|gb|CK063270.1|CK063270
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|58663954|gb|CK052640.1|CK052640
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|87037802|gb|CI192424.1|CI192424
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|27921032|gb|CB096840.1|CB096840
EST:     CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: CTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
EST: gi|87016380|gb|CI273590.1|CI273590
EST:     GGCGATGATGAG                         TTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT
genomic: GGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGT

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 1 RNA-Seqlibrary.


Block sizes: 65 (upstream exon), 60 (downstream exon)
Score: 23

TGGTCGGAGTTTTGGATCCCATGAGGACGAAGACAGGAGTTCAGGGAACCCTCAATCTGGGAAAGCACTGTATGACTTCACAGCAGGTGGCGATGATGAGgtatggaggc ... tttctttcagTTGAGTTTAACTGCTGGAGAAGATGTGGAAATCGAATATGAGGTCGATGGTTGGTACTAT




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