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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTCCACTTGTCAAGATCGAAAAATTTGAAGTTGTTGCCAAGAAAATTTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactattgaactatgtgaagcatatagcatttattgtgtttgatttcaattctaatcatatgaagcagtgtaatttgcataagaaagccttttcccc...

Basic information

species Oryza sativa
transcript LOC_Os04g32650.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32650.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 8
GTCTTTCCACTTGTCAAGATCGAAAAATTTGAAGTTGTTGCCAAGAAAATTTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactattgaactatgtgaa--gcatatagcatttattgtgtt--tgatttcaattctaatcatatgaagcagtgtaatttg---cataagaaagccttttcccc-----------------
||||||||| | |||||| |||| |||||||| | |||||||||||| || || || ||  |||||||||| |||||||| || || || || ||||||||||||      ||  |   ||   ||   |    | | | |   |  | || | | ||||  |   ||| ||   |  | |||    | |    ||  ||  |||                   
GTCTTTCCATTGGTCAAGCTCGAGAAATTTGAGGCTGTTGCCAAGAAGATCTCCAAGGCCCTGACAGCAGCTGGGATTTCACATATCATCGACATGACAGgtacatggccaaatcagtagagttgcgcttgttttctgtggcactgtttatctaagttctgttgcaatggaggtctacagtttcagtcgttctgaattctgatccgtgactgcctctgttgcag
















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|88224539|gb|CI222719.1|CI222719
EST:     TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|88220982|gb|CI220938.1|CI220938
EST:     AGCAGCAGGGATTTCTCACATGATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCGC
genomic: AGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|86416118|gb|CI030129.1|CI030129
EST:     TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAG                         GTAACACTATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|218493281|gb|FG957986.1|FG957986
EST:     CTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: CTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|29624770|gb|CB629781.1|CB629781
EST:     TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|86426089|gb|CI071186.1|CI071186
EST:     CTCACATAATTGATATGACAG                         GTAACACTATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: CTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|86425972|gb|CI071069.1|CI071069
EST:     TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|29617709|gb|CB622721.1|CB622721
EST:     TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|86253665|gb|CI014298.1|CI014298
EST:     TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|109712894|gb|CI105502.1|CI105502
EST:     GGATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCTC
genomic: GGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|88219212|gb|CI220485.1|CI220485
EST:     TCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCTC
genomic: TCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|29639396|gb|CB644405.1|CB644405
EST:     TTTGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|89198865|gb|CI003602.1|CI003602
EST:     ATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: ATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
EST: gi|29658006|gb|CB654281.1|CB654281
EST:     TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAG                         GTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC
genomic: TTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCC

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: 74 (upstream exon), 70 (downstream exon)
Score: 34

GTCTTTCCACTTGTCAAGATCGAAAAATTTGAAGTTGTTGCCAAGAAAATTTCGAAAGCATTGACAGCAGCAGGGATTTCTCACATAATTGATATGACAGgtacactatt ... gttgttgcagGTAACACAATCGGTAAGCGTTATGCAAGGACCGATGAAATCGGTGTCCCCCTGGCAATCACGGTTGACAACACCACGAGTGTGACTGTCCGTGACCGGGA




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