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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtag

Basic information

species Oryza sativa
transcript LOC_Os07g37740.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G448715_T02 (Zea mays), 5'ss of exon 8
GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttctgcgaacttctc---------cgtgctttt----------cttgtgtatatgagtaagtaacatttattggacacttgttttgtag
| || ||||| |||||  ||||||| || |||||||| ||||| |||||||||||||||||||| |||||||| |||||||||||||| |||||||| | | | ||  | ||  ||          |||| | |           |||| |  |||  || ||||  |||| |||  |||||||||||||
GTGTTAAGATCTGGTTATTGGCAATAATTTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTGTATAATGCAATGAGgtaatttatttgaaatctcatcacattattttgtgcctctaccatatatctttgtatgcatggataggtaatgtttactggcaacttgttttgtag

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 8
GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttctgcgaactt---------ctccgtgc--------ttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtag
|||| ||||| |||||| ||||||| ||||||||||| ||||| |||||||||||||||||||| |||||||| ||||| |||||||| |||||||||| | | ||  | ||           |  ||||        |||| |||| |  |    || ||||   ||  |||  |||||||||| ||
GCGTTAAGATCTGGTTGTTGGCAATAATCTACTTCATATCTGGTGTTCCTGGTGCATATGTTTTGTGGTATCGTCCTCTATATAATGCAATGAGgtattttatttgaaatctcattacattattttgtgcatctaccatttttttgtatgcacatataggtaatgcttgctggcaacttgttttgcag

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 5'ss of exon 7
GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttctgc---gaacttctccgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtag------------------------------------------------------------------------------------
|    |  |||||||| || || || ||||| ||||| || ||||||||||| || |||||| | |||||||| ||||| |||  ||| ||||||||||  | |  |     | || ||| |     | |  | | |   | |  ||  | | | ||   |  || ||| |  |                                                                                    
GTCCAACAATATGGTTTCTAGCTATTATCTATTTCATATCAGGGGTTCCTGGAGCGTATGTTATGTGGTATCGCCCTCTTTATCGTGCCATGAGgtattcatgccacttaagatttttcctttaaaatatcttatctgctactgcgt--cgtgtgtt---cctttatttagagggaaaacaaaaagagtattccagatagcatcgtagttaagagtcaaaactttcattgagatgtgtgttgatttggttgtgtgcag

upper sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ29726 (Selaginella moellendorffii), 5'ss of exon 4
------GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttctgcgaacttctccgtgcttttcttgtgtatatgagtaagtaacatttattggacacttgttttgtag
      | ||  | || ||||| || || ||||| ||| |  |  ||||  |||| ||  | ||||   | ||||||||||||||||| ||||| |||||||||||| |  |  |   || | |  | ||||||  |    |  |    |                           
CCGCAGGTGTCCAAATCTGGTTCCTCGCGATCATTTACATGCTAGCTGGAATTCCCGGATCGTATGGACTGTGGTATCGACCTCTGTACAATGCAATGAGgtattgtgt--gtcactctcacgggacgtttcttcagctcgtttgcttttccag-----------------------

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|86430196|gb|CI082619.1|CI082619
EST:     CATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: CATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|66923956|gb|CX110804.1|CX110804
EST:     GTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: GTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|86429939|gb|CI082362.1|CI082362
EST:     TCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: TCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|87027955|gb|CI276311.1|CI276311
EST:     ATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: ATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|58683369|gb|CK072056.1|CK072056
EST:     GTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: GTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
EST: gi|88966183|gb|CI013059.1|CI013059
EST:     GTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAG                         GACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG
genomic: GTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG

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: 70 (upstream exon), 43 (downstream exon)
Score: 20

GCGTGAAGATATGGTTGCTGGCAATCATCTACTTCATCTCTGGGGTTCCTGGTGCATATGTTTTATGGTATCGACCTCTGTATAATGCTATGAGgtattgtttc ... tgttttgtagGACTGATAGTGCCTTGAAGTTTGGATTGTTCTTCTTGGTTTACCTG




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