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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaaattctcatatttattctatttagagcgtttggacatcaccaattcaccatgaaatgggaagcgtcttttattttccctcttacaaacaat...

Basic information

species Oryza sativa
transcript LOC_Os09g12660.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12660.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G106213_T02 (Zea mays), 5'ss of exon 9
--TGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaaattctcatatttattctatttagagcgtttggacatcaccaattcaccatgaaatgggaagcgtcttttattttccctcttacaaacaat-
   ||||| || ||||||||||| |||||||| ||||| || || || ||||| ||||| |||||| |||||||||| || |||| ||||| |||| |||||||  | ||   |      |   | | | ||||  |   | | ||     ||       |  |  |      | || | |     |    |||     | | 
GAAGGATATTTTATCAAAAGTGGAATTGTCACGGTGATTAAAGATGCTTTAATTCCTAGTGGAACAATCATATAAAGTCAGCCAA-CACCA-TGTATATAAGgtcatatctc-tagcagaaaccagtgtttttatggttgtcgtactcgtacatagggttactagcttttgctcttcatattgcaactggattaagcttactg
















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|87009864|gb|CI277365.1|CI277365
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|86500004|gb|CI142637.1|CI142637
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|88849769|gb|CI001475.1|CI001475
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|30228286|gb|CB966177.1|CB966177
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCA-T
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|86496727|gb|CI139360.1|CI139360
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|86494922|gb|CI137555.1|CI137555
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|87010148|gb|CI279245.1|CI279245
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|89164207|gb|CI101295.1|CI101295
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|88967313|gb|CI002497.1|CI002497
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|88225908|gb|CI225824.1|CI225824
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|86500640|gb|CI143273.1|CI143273
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|86504994|gb|CI147627.1|CI147627
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGCCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|86504993|gb|CI147626.1|CI147626
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGCCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|58683758|gb|CK072445.1|CK072445
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|86858990|gb|CI275175.1|CI275175
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|87018057|gb|CI275871.1|CI275871
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|88227669|gb|CI227149.1|CI227149
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|86488092|gb|CI130725.1|CI130725
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGCCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|88222446|gb|CI222402.1|CI222402
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|218485015|gb|FG946141.1|FG946141
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|29675781|gb|CB672056.1|CB672056
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|88222920|gb|CI220666.1|CI220666
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
EST: gi|88957454|gb|CI095395.1|CI095395
EST:     TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAG                         GTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT
genomic: TCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAAT

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), 74 (downstream exon)
Score: 63

TGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTAGCGGAACAGTCATATAAAGGCAACCAATCACCACTGTACATAAGgttctctcaa ... tgtaatgcagGTTGGGCCTTGCAGCATATGGTGATCTGATCTCCAGTGCACATCAAGCAATCAACTTTTAACGCTGTGGTTTATTCCATGCTGCCAGTTCACCAAGCTCT




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