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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTGGCAGCCATACCCTCAATTGACAGTGAAGCCGTCCAACAGAGAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccactaactgcttacatgctacccctattcgtaccttccatctttcttacccatttctccatctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g22864.1
intron # 24
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g22864.2 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G327394_T01 (Zea mays), 5'ss of exon 24
GCTCTGGCAGCCATACCCTCAATTGACAGTGAAGCCGTCCAACAGAGAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccactaactgcttaca-tgctacccctattcgtaccttccatctttcttac-ccatttctccatctgcag
||||| ||||||||||| ||||| || |||||||| ||||||||| || | ||||| ||||| || ||||| ||  | || ||||||||||| |||||  |   |     | |||   |   |  || | || | |  |   | ||  |||| | | | ||   | |||||
GCTCTTGCAGCCATACCTTCAATAGATAGTGAAGCAGTCCAACAGCGATTGGATCGCGTTCGAACGTTCTATGAGTTGTTAAATTTGCCTTTTGAGgtacatgtcacttagtttatggtaacaatccaagtctttcgatgttttttatttacactactgctatgtttgcag
















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|86853148|gb|CI324850.1|CI324850
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|86437704|gb|CI119624.1|CI119624
EST:     GAATAGATCGTGTCCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|29624113|gb|CB629124.1|CB629124
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|88269996|gb|CI381294.1|CI381294
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|58586846|gb|CF985154.1|CF985154
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|88382101|gb|CI533305.1|CI533305
EST:     GAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|86603014|gb|CI357378.1|CI357378
EST:     ACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: ACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|86480164|gb|CI122797.1|CI122797
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|29626007|gb|CB631018.1|CB631018
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|86480174|gb|CI122807.1|CI122807
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|88670678|gb|CI724794.1|CI724794
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|88671305|gb|CI724351.1|CI724351
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATNTATTTCCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|58692351|gb|CK081038.1|CK081038
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|86437028|gb|CI118750.1|CI118750
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|88253653|gb|CI352279.1|CI352279
EST:     AACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: AACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
EST: gi|88996514|gb|CI260018.1|CI260018
EST:     GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAG                         TCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA
genomic: GAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA

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: 63 (upstream exon), 72 (downstream exon)
Score: 16

GCTCTGGCAGCCATACCCTCAATTGACAGTGAAGCCGTCCAACAGAGAATAGATCGTGTTCGGACATTCTACGAACTCTTGAATTTGCCTTTCGAGgtttaccact ... ccatctgcagTCTTTGCTTGGATTTATTGCAGAACATGAATATTTATTTTCTGCAAAAGA




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