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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGCAGTGAGCAAGAACATGGTGGAGAGCCTCGCGGTGCCCGCATTCCGTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAGgtgctatacctttggagactttgggggtggcagtgcttaacctcctgtgatggtttattacattttggtcattttgttgattgttggggttgatttggtttggttag

Basic information

species Oryza sativa
transcript LOC_Os08g33440.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G117786_T01 (Zea mays), 5'ss of exon 1
GGCTGCAGTGAGCAAGAACATGGTGGAGAGCCTCGCGGTGCCCGCATTCCGTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAGgtgctatacctttggagactttgggggtggcagtgctt-aacctcctgtgatggtttattacattttggtcattttgttgattgttggggttgatttggtttggttag
||||||||||||||||||||||||||||||||| || ||||| |||||||| || || ||||| ||||| |||||||||||||||||||| || || ||||||       |||||||      ||  || | |  ||| || ||||| ||    ||| |        | |  |  || | | | |||||  ||||||| ||| |  ||
GGCTGCAGTGAGCAAGAACATGGTGGAGAGCCTGGCAGTGCCAGCATTCCGCGTTGGGTACCCCATTGTAACCGATAAGCTCGATGAGCTGTACGAAAAGgtgagg---atttggag----caggcatgactgcacttgaagctcctttg----tttttcttgccccgct--tcctgattactattggg-ctgatttgattttgacag

upper sequence: LOC_Os08g33440.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 1
GGCTGCAGTGAGCAAGAACATGGTGGAGAGCCTCGCGGTGCCCGCATTCCGTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAGgtgctatacctttggagactttgggggtggcagtgcttaacctcctgtgatggtttattacattttggtcattttgttgattgttggggttgatttggtttggttag
|||||||||||||||||||||||||||||| || || ||||| |||||||| || || ||||| ||| | || ||||| ||||| ||||| ||||| |||||             ||  ||||  |  ||      | |  ||||| ||    |||     |   || |  |  || | | |  |  |  ||||||| ||| |  ||
GGCTGCAGTGAGCAAGAACATGGTGGAGAGTCTGGCAGTGCCAGCATTCCGCGTTGGGTACCCCATTATTACTGATAAACTCGACGAGCTGTATGAAAAGgta------------aggatttgaagcagggcaccttgaggctcctttg----ttttccttagcctgct--tcctgattactaattagactgatttgattttgacag
















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|58585893|gb|CF984201.1|CF984201
EST:     CGATGAGCTATATGAGAAG                         GTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
genomic: CGATGAGCTATATGAGAAGgtgctatacc ... gtttggttagGTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
EST: gi|88584205|gb|CI701741.1|CI701741
EST:     GTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAG                         GTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
genomic: GTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAGgtgctatacc ... gtttggttagGTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
EST: gi|88365470|gb|CI680109.1|CI680109
EST:     GTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAG                         GTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
genomic: GTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAGgtgctatacc ... gtttggttagGTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
EST: gi|66912791|gb|CX099639.1|CX099639
EST:     GTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAG                         GTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
genomic: GTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAGgtgctatacc ... gtttggttagGTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
EST: gi|58688879|gb|CK077566.1|CK077566
EST:     GTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAG                         GTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT
genomic: GTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAGgtgctatacc ... gtttggttagGTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCT

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: 75 (upstream exon), 72 (downstream exon)
Score: 57

GGCTGCAGTGAGCAAGAACATGGTGGAGAGCCTCGCGGTGCCCGCATTCCGTGTGGGATACCCAATTGTGACCGATAAGCTCGATGAGCTATATGAGAAGgtgctatacc ... gtttggttagGTCAAGTCAAAGGGGGTGACCATGACAGTTCTGCTGGCGAAGGCCGCAGCTATGGCACTTGCGCAGCACCCGGTGGTGAATGCTAGCTGCAGGGATGGGA




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