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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcaaccatcaaatgttatgccttaaattgtaaaatttcttctttgcgcttgacatgaattactgctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCTGATATCATAGACTACCTGAGGGCCACATATGCGGCTTGAGAATCCCTTC

Basic information

species Oryza sativa
transcript LOC_Os08g44400.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44400.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G022866_T02 (Zea mays), 3'ss of exon 11
---------------------------------------gttgg-caaccatcaaatgttatgccttaaattgtaaaatttcttctttgcgcttg-acatgaattactgctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCTGATATCATAGACTACCTGAGGGCCACATATGCGGCTTGAG-AATCCCTTC
                                       | ||  ||  | |   || |     | |    ||  | ||    | | || |  ||    ||  ||||||   |||||||| || || ||||||||||||||||| || ||| ||||||| || |||||||| |||||||||||||||| ||| ||||||||    |    || | | | 
gtaggacgccttgctataacgctattgatgcctttcgacgctgaacattcttttgatttgcctgcctggtgtgcgacatcatgtatgtgtgtgtgtgtgtgtgttactgtgttggcagGCGCCGTACATCGAAGATCCTAACACGGGAGTCCAGATGTTTGAAAGCGCTGAAATCATAGACTACCTGAAGGCAACATATGCCCTGTACCCAAGCTCGT-

upper sequence: LOC_Os08g44400.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G825090_T02 (Zea mays), 3'ss of exon 12
--------------------------------------gttgg-caaccatcaaatgttatgccttaaattgtaaaatttcttctttgcgcttg-acatgaattactgctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCTGATATCATAGACTACCTGAGGGCCACATATGCGGCTTGAG-AATCCCTTC
                                      | ||  ||  | |   || |     | |    ||  | ||    | | || |  ||   |||  ||||||   |||||||| || || ||||||||||||||||| || ||| ||||||| || |||||||| |||||||||||||||| ||| ||||||||    |    || | | | 
gtaggacgccttgctataacgctattgatgcatttgacgctgaacattcttttgatttgcctgcctggtgtgcgacatcatgtatatgtgtgtgtgtatgtgttactgtgttggcagGCGCCGTACATCGAAGATCCTAACACGGGAGTCCAGATGTTTGAAAGCGCTGAAATCATAGACTACCTGAAGGCAACATATGCCCTGTACCCAAGCTCGT-

upper sequence: LOC_Os08g44400.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G085000_T02 (Zea mays), 3'ss of exon 10
---------------gttggcaaccatcaaatgttat-gccttaaattgtaaaatttcttctttgcgcttgacat--gaattactgctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCTGATATCATAGACTACCTGAGGGCCACATATGCGGCTTGAGAATCCCTTC
                |||    |  | |      |  | ||| | |||      |  |   |  |     | ||  | ||||||    |||||||| ||||| ||||||||||||||||| || ||| |||||||||| ||||| || |||||||||||||||| ||| |||||||     |   ||  |    
gtacgaggccatgctattgatgcctttgacgctgaacagtcttgatttgcctgtctagtgtgtgacatcatatatttgcattactatattggcagGCGCCTTACATCGAAGATCCTAACACGGGAGTCCAGATGTTCGAAAGCGCAGAAATCATAGACTACCTGAAGGCAACATATGTCCTGTACCAAAGCTCAT

upper sequence: LOC_Os08g44400.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G825090_T05 (Zea mays), 3'ss of exon 11
--------------------------------------gttgg-caaccatcaaatgttatgccttaaattgtaaaatttcttctttgcgcttgacatgaattactgctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCTGATATCATAGACTACCTGAGGGCCACATATGCGGCTTGAG-AATCCCTTC
                                      | ||  ||  | |   || |     | |    ||  | ||    | | || |  ||  |||  ||||||   |||||||| || || ||||||||||||||||| || ||| ||||||| || |||||||| |||||||||||||||| ||| ||||||||    |    || | | | 
gtaggacgccttgctaaaacgctattgatgcatttgacgctgaacattcttttgatttgcctgcctggtgtgcgacatcatgtatatgtgtgtg-tatgtgttactgtgttggcagGCGCCGTACATCGAAGATCCTAACACGGGAGTCCAGATGTTTGAAAGCGCTGAAATCATAGACTACCTGAAGGCAACATATGCCCTGTACCCAAGCTCGT-

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|88320401|gb|CI523144.1|CI523144
EST:     GAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88459668|gb|CI521928.1|CI521928
EST:     GCGGCAGCCCCAGGAGACATGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88528036|gb|CI456238.1|CI456238
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTGCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGTTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|86482838|gb|CI125471.1|CI125471
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACTGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88527164|gb|CI455292.1|CI455292
EST:     AGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: AGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88536787|gb|CI464575.1|CI464575
EST:     GCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT

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: 58 (upstream exon), 73 (downstream exon)
Score: 47

CACTACACTCTTGGAGTAACTGGTAGCTGAAAATTTCTGCAGCTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCTGATATCATAGACTACCTGAGGGCCACATATGCGGCTTGAGAATCCCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttaaattgtaaaatttcttctttgcgcttgacatgaattactgctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCTGATATCATAGACTACCTGAGGGCCACATATGCGGCTTGAGAATCCCTTC
                            gcttgac  putative branch site (score: 47)
     aaattgtaaaatttct  TA-rich tract