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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACTGAACTTGTTGAGCATGTTCTTAATGACTGTGACATTGTTGGTAAAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgttaacagtctgtggtaattttggatgtaataatccccttacatcatttttgtcttgtgtgtag

Basic information

species Oryza sativa
transcript LOC_Os01g40340.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G149321_T01 (Zea mays), 5'ss of exon 4
AAGAACTGAACTTGTTGAGCATGTTCTTAATGACTGTGACATTGTTGGTAAAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgttaacagtctgtggtaattttggatgtaataat-----ccccttacatcatttttgtcttgtgtgtag-----------
|||| ||||| ||||||||||||||||| |||| ||||| ||||||||||||||||||| | | || |   |||| || ||||| || ||||||| ||||||||||| | || |  ||||    |||||  |  | || |      ||   | | |  || || ||| ||||||             
AAGACCTGAAGTTGTTGAGCATGTTCTTCATGAATGTGATATTGTTGGTAAAATTCTTGTCTCAGAGAGGTTTTCATCCTTGTCGACTGAGTCTAATGGGgtaagttatcaatacactgtaactattttttactttatcacagagacctaatccctttttattttctggtgtgtcttctatgctcag
















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|58691100|gb|CK079787.1|CK079787
EST:     ACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: ACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|29612947|gb|CB617960.1|CB617960
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|29680806|gb|CB677081.1|CB677081
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|88717309|gb|CI740819.1|CI740819
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|58679221|gb|CK067908.1|CK067908
EST:     GGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: GGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|29680847|gb|CB677122.1|CB677122
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|88417264|gb|CI576338.1|CI576338
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
EST: gi|58689270|gb|CK077957.1|CK077957
EST:     AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGG                         CCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT
genomic: AAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGT

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: 60 (upstream exon), 50 (downstream exon)
Score: 16

AAGAACTGAACTTGTTGAGCATGTTCTTAATGACTGTGACATTGTTGGTAAAATTCTTGCCGCGGAAAAACTTTCTTCTTTGTCAACAGAGTCTACTGGGgtaagttgtt ... ttgtgtgtagCCTACTATACCTTCAGATGGTAAATCGATTCCCAAAATTGGGAATATTGGTCACATGACAAGAATAACCAACAAGCTTATTCAGTTGGGAAGCAGTAACG




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