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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatggatgtgaggttctcaattgtgtcgagcccggtgaaatgtaagatgtgagcactgaacactaaggtctctctggccatcgattctgcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGATGTGTACAGCTTCGGGATCCTGATAATGGAAATCATCTCCGGTCGAAGC

Basic information

species Oryza sativa
transcript LOC_Os05g36050.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G147051_T01 (Zea mays), 3'ss of exon 2
------gtaagatg--gatgtg----aggttctcaattgtgtcgagcccggtgaaatgtaagatgtgagcactgaacactaaggtctctctggccatcgattctgcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGATGTGTACAGCTTCGGGATCCTGATAATGGAAATCATCTCCGGTCGAAGC
      || ||  |  |  |||    |  || | |  |   ||    |||| |  |  | | ||||   |  |  |    |  ||  || |         || |   || | || || || || || |||||||| |||||||| |||||||| ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||
gtgggtgtgagccgccgccgtgcttaaaattttgagcttcttcccttccggggtgaaatgaaatgt--ccgatcgatgtgagagttcctttc--------ttttttgttggaagCTACGTGGCGCCAGAGTACGCTAGCACCGGCATGCTGAACGAGAGGAGCGACGTGTACAGCTTCGGGATCCTGATCATGGAGATCATCTCCGGCCGAAGC

upper sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S358_6V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------gtaagatggat-gtgaggttct-----caattgtgtcgagcc-cggtgaaatgtaagatgtgagcactgaacactaaggtctctctg-gccat--cgatt-ctgcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGATGTGTACAGCTTCGGGATCCTGATAATGGAAATCATCTCCGGTCGAAGC
           ||| |||  || |    ||| |      |||||   | |||  |||||| | ||   || ||         ||      ||||  || | | |  ||||   ||  ||||||| |||||||| || |||||||||| ||| ||  ||||||| ||| |||| |||||||||||||| ||| | ||  | ||||| || ||| |||| |||   
gtaagcgtaaagtatgatttattgcctcgttgtaacaataattgcagctagcaacggtgacaagt---atttgtttgtctttcatggttttctccttgagtcgttacgatggttgtttttgcagGTATGTAGCCCCCGAGTACGCGAACACGGGCCTGCTGAACGAGCGAAGTGATGTGTACAGCTTTGGGGTGCTTCTCATGGAGATTATCACCGGGCGAGAT

upper sequence: LOC_Os05g36050.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S568_2V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------gtaagatggatgtgaggttctcaattgtgtcgagcccggtgaaatgtaagatgtgagca-ctgaacactaaggtctctctggccatcgatt--ctgcatt-tgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGATGTGTACAGCTTCGGGATCCTGATAATGGAAATCATCTCCGGTCGAAGC
                                                          |||   | || | | ||   | |||   || || |   | |  | || |  | | |   || |||  |   ||| |  |  ||||   ||  ||| ||    ||| || ||||| ||||||||||||| ||| ||  ||||||||||| ||||||||||||||||||| ||| | ||  | ||||| |||||| | || |||   
gtaagctcaaggccctcctctggattgtattgtattgttgaaacagtagttgcagttataaacggcatttaatgt---cgatttcttctagtcacat-agttttatgtcgcgtgtttctcaacgttctagtccccatccccattctttggctgtatcactcagGTACGTAGCGCCGGAGTACGCGAACACGGGCCTGCTGAATGAGCGAAGCGATGTGTACAGCTTTGGGGTGCTTCTCATGGAGATCATCACGGGGCGAGAT

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|58596637|gb|CK007165.1|CK007165
EST:     CTCGGTTCAGACAGCAACTATGTTACCACGAGAGTCATGGGAACATTTGG                         TTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
genomic: CTCGGTTCAGACAACAACTATGTTACCACGAGAGTCATGGGAACATTTGGgtaagatgga ... gcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
EST: gi|117238335|gb|CT862171.1|CT862171
EST:     CTCGGTTCAGACAGCAACTATGTTACCACGAGAGTCATGGGAACATTTGG                         TTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
genomic: CTCGGTTCAGACAACAACTATGTTACCACGAGAGTCATGGGAACATTTGGgtaagatgga ... gcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
EST: gi|58653268|gb|CK041948.1|CK041948
EST:     CTCGGTTCAGACAGCAACTATGTTACCACGAGAGTCATGGGAACATTTGG                         TTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGA
genomic: CTCGGTTCAGACAACAACTATGTTACCACGAGAGTCATGGGAACATTTGGgtaagatgga ... gcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGA
EST: gi|58599417|gb|CK009945.1|CK009945
EST:     CTCGGTTCAGACAGCAACTATGTTACCACGAGAGTCATGGGAACATTTGG                         TTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
genomic: CTCGGTTCAGACAACAACTATGTTACCACGAGAGTCATGGGAACATTTGGgtaagatgga ... gcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
EST: gi|58665151|gb|CK053837.1|CK053837
EST:     CTCGGTTCAGACAGCAACTATGTTACCACGAGAGTCATGGGAACATTTGG                         TTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
genomic: CTCGGTTCAGACAACAACTATGTTACCACGAGAGTCATGGGAACATTTGGgtaagatgga ... gcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
EST: gi|58685024|gb|CK073711.1|CK073711
EST:     CTCGGTTCAGACAGCAACTATGTTACCACGAGAGTCATGGGAACATTTGG                         TTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA
genomic: CTCGGTTCAGACAACAACTATGTTACCACGAGAGTCATGGGAACATTTGGgtaagatgga ... gcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGA

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: 71 (upstream exon), 62 (downstream exon)
Score: 12

TGGACAAGAGATGGAACCCCAAGGTCTCGGACTTTGGCCTCGCCAAGCTCCTCGGTTCAGACAACAACTATGTTACCACGAGAGTCATGGGAACATTTGGgtaagatgga ... gcatttgcagTTATGTAGCACCGGAGTACGCGAGCACCGGGATGCTGAATGAGAGAAGCGATGTGTACAGCTTCGGGATCCTGATAATGGAAATCATCTCCGGTCGAAGC




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