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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATTTGGAGCATTGTTTGCTTCCATCCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttaccctgcgccatctgatgcgagtaaatacgccactgtttttgttcttgtctcacacatttgctttgtttgactttcag

Basic information

species Oryza sativa
transcript LOC_Os01g55500.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55500.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G437859_T04 (Zea mays), 5'ss of exon 12
GAAAATTTGGAGCATTGTTTGCTTCCATCCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttaccctgcgccat--ctgatg-cgagtaaatacgccactgtttttgttcttgtctcacacatttgctttgtt-tgactttcag
| ||||||||||| ||||| ||||||||||| || ||||||||||||||||||||||||||| |||| || ||||||||||||| | ||||   | |  ||||||  | |       |  |     |    |  || ||         |||||  | ||||| ||||
GGAAATTTGGAGCCTTGTTCGCTTCCATCCCGTTCACCATCTTTGCGGCCGTGTACTGCGTCCTGTTCGGGCTAGTTGgttggtcatcctgtttccttcctgatgatgtgctttggtgtaatgcaatgcaatgctgcctgggctgacggcttttctctgactctcag
















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|58669485|gb|CK058171.1|CK058171
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
EST: gi|33793472|gb|CF322619.1|CF322619
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
EST: gi|25807066|gb|CA763027.1|CA763027
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
EST: gi|87026155|gb|CI256898.1|CI256898
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
EST: gi|58670557|gb|CK059243.1|CK059243
EST:     CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTG                         CGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA
genomic: CCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCA

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: 72 (upstream exon), 66 (downstream exon)
Score: 22

GAAAATTTGGAGCATTGTTTGCTTCCATCCCATTTACCATCTTTGCGGCCGTGTACTGCGTCTTGTTTGGACTAGTTGgttggttacc ... tgactttcagCGGCAGTGGGGCTCTCCTTCTTGCAGTTTACTAACATGAACTCCATGCGCAACCTCTTTATCGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGA




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