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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctctaaacttcatgatttttccttctgcagagccattgatcgtaaaccatttatcctgtttgtag

Basic information

species Oryza sativa
transcript LOC_Os05g07130.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.2 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G021846_T02 (Zea mays), 5'ss of exon 20
ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctctaaacttcatgattttt---------------ccttctgcagagcca-ttgatcgtaaaccatttatcctgtttgtag
 |||||||| || ||||| ||||||||||||||||| |||||||| || || || || || |||||||||    | | || ||||  | |               |   | ||||| | | ||  |  | ||| |||| |||  ||  |||
GCTGGAACCCGTCATCATCGAGCTAGAACGCCAGCGTGCACCAGTGGTTGTCATATCTCATCAGgtaaattgtcatagttgatgaaatattggaaagttggagcgcggacagcagaactagttagttttgaactatttgtcccattgctag
















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|58611022|gb|CK038734.1|CK038734
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|86850852|gb|CI338828.1|CI338828
EST:     CATTGAGCTAGAACGCCAGCGAGCACCACGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTTACAGGCCTCTGAGGGAA
genomic: CATTGAGCTAGAACGCCAGCGAGCACCA-GTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|29629510|gb|CB634519.1|CB634519
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|29616012|gb|CB621024.1|CB621024
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|16578926|gb|BI813021.1|BI813021
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|86842389|gb|CI335281.1|CI335281
EST:     TGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTACGGGCGCTATATGCATATTTCGCTGACAGGGCCTCTGAGGGA
genomic: TGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACA-GGCCTCTGAGGGA
EST: gi|86838836|gb|CI330278.1|CI330278
EST:     CATTGAGCTAGAACGCCAGCGAGCACCAGTAGGTCGTTATTTCCCACCAGG                         GCTGTATTGCGGGCGCTATATGCATATTTCCCTGACAGGCCTCTGA-GGA
genomic: CATTGAGCTAGAACGCCAGCGAGCACCAGTA-GTCGTTATTTCCCACCA-Ggtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGA
EST: gi|29612782|gb|CB617795.1|CB617795
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|29615977|gb|CB620989.1|CB620989
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|86868850|gb|CI334222.1|CI334222
EST:     GCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: GCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|86853669|gb|CI330520.1|CI330520
EST:     TCATTGAGGTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGCCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|88844562|gb|CI020409.1|CI020409
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|29615975|gb|CB620987.1|CB620987
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|29616052|gb|CB621064.1|CB621064
EST:     TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAG                         GCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA
EST: gi|86869030|gb|CI335597.1|CI335597
EST:     TCATTGAGCTA-AACGCCAGCGAGCACCACTAGTCGTTATTTCCCACCAG                         GCTGGATTGCGGGCGCTATATCCATATTTCGCTCACAGGCCTCTGAGGGAA
genomic: TCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAA

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: 64 (upstream exon), 66 (downstream exon)
Score: 28

ACTGGAACCTGTTATCATTGAGCTAGAACGCCAGCGAGCACCAGTAGTCGTTATTTCCCACCAGgtaaatctct ... ctgtttgtagGCTGTATTGCGGGCGCTATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG




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