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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCCGCCGCCTCTCCCGACCCTCCACCTCCTCGTCTTCCTCCGCGCACTCCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcctctgttcgaatcgcctccatgatctccagatccatctcgtccggttcttacggtgaaatggattgcgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g49770.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49770.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G157172_T02 (Zea mays), 5'ss of exon 1
------CCTCCGCCGCCTCTCCCGACCCTCCACCTCCTCGTCTTCCTCCGCGCACTCCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcctctgttc-gaatcgcctccatgatctccagatccatctcgtccggttcttacg-gtgaaatgga---ttgcgtgtgcag
      |||||||||||||  ||| |||||| ||| |||| | |||      ||||||||||| |||||||  || || || || ||||||||||| ||||||||||||  |       |  | |   | ||| | ||||| |||||||||| ||||    | |   |  || ||   ||   ||||||||| ||
GGAGTCCCTCCGCCGCCTCAACCGCCCCTCCGCCTTCTCGCCGTCC------CACTCCAACGGCCACCACCACCCTCGAAATCCCATCGGCGAAATCCACCTCAAGgtcctcggttctggccctgtgcctccttcgtgatcgccagatccatttcgtgttctgccagcttgttaacgcgacccttgcgtgtgtag

upper sequence: LOC_Os03g49770.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G147332_T01 (Zea mays), 5'ss of exon 1
------CCTCCGCCGCCTCTCCCGACCCTCCACCTCCTCGTCTTCCTCCGCGCACTCCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcctctgttcgaatcgcctccatgatctccagatccatctcgtccggttc----ttacggtgaaatggattgcgtgtgcag
      |||||||||||||  ||| ||||||||||||||||| |||      ||||||||||| |||||||  || || || || ||||||||||| ||||||||||||        | ||||    ||||||| ||||| |||||||||  ||||| | | |    || |      |  | ||||||||||||
TGATTCCCTCCGCCGCCTCAACCGCCCCTCCACCTCCTCGTCGTCC------CACTCCAACGGCCACCACCATCCTCGAAACCCCATCGGCGAAATCCACCTCAAGgtc------tccggttcttgccgcctccgtgatcgccagatccacttcgtctgttgccagcttgctaaaggagcggttgcgtgtgcag
















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|29636164|gb|CB641173.1|CB641173
EST:     CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAG                         GTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC
genomic: CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcc ... gcgtgtgcagGTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC
EST: gi|29636220|gb|CB641229.1|CB641229
EST:     CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAG                         GTGTCGTCCGTGCGGGAGAGCANATCGGATGACAGGAGGTTCTCGATCTTC
genomic: CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcc ... gcgtgtgcagGTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC
EST: gi|88411940|gb|CI566669.1|CI566669
EST:     CCAACGGTCACCAACTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAG                         GTGTCGTTCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC
genomic: CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcc ... gcgtgtgcagGTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC
EST: gi|29634233|gb|CB639242.1|CB639242
EST:     CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAG                         GTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC
genomic: CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcc ... gcgtgtgcagGTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC
EST: gi|29633376|gb|CB638385.1|CB638385
EST:     CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAG                         GTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC
genomic: CCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcc ... gcgtgtgcagGTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTC

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: 70 (upstream exon), 52 (downstream exon)
Score: 5

CCTCCGCCGCCTCTCCCGACCCTCCACCTCCTCGTCTTCCTCCGCGCACTCCAACGGTCACCACCTACCCCGCAAGCCTATCGGCGAAATTCACCTCAAGgtcagcatcc ... gcgtgtgcagGTGTCGTCCGTGCGGGAGAGCAGATCGGATGACAGGAGGTTCTCGATCTTCTCGGGGACGAAGAGGCTGCACCTCCGGGCGGAGACAAGGGAGGACAGGG




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