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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgctacag

Basic information

species Oryza sativa
transcript LOC_Os02g56000.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G027282_T01 (Zea mays), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgcaac--tagacatattattgttcacagtataataaactgtaattttttcctgctacag------------
| ||||||||  | ||||| ||||||||||| ||||||||| |||| |||||||| ||||||||||||||||| || |||||||||||||||||||| ||||||||||   |||   ||| |||     |  ||       | ||  |   || |   || |  |   ||| |     |  || || |             
CTAAGCTTGTTAGAGATGCTTTTCAGCTTGCTAAGGAGAAAGCCCCGTGCATCATCTTTATTGATGAAATTGATGCCATTGGAACAAAGCGTTTTGACAGgtacattttttatttagtttgtcatccagtctaatgtctttcctaacaccttttaacctacatcagtttgtgaccaagtt-tgatagacattttaacaagc

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G29250.1 (Glycine max), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtac-atttagcattgtctttatca-atgcatgcaactagacatattattgttcac---agtataataaactgtaattttttcctgctacag------------------------------------------
|||| ||||| |||||||||||||| || ||||| ||||| || || ||||| |||||||| ||||||||||| |||||||| ||||||||||||||||||||  |  | ||| |   ||    | |    ||||| |     | || ||  |      ||    | | |    | | ||     | || |                                           
CAAAACTTGTTCGTGATGCCTTTCAACTAGCAAAAGAGAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTGGTACAAAGCGTTTTGATAGgtattagctggcagtaatttagatatacatttgcaattgacttttttctttcttttttgaggtagagagatcagagtgttacttagttaaattgtctcggttctaactttgatgtatcttgtggctaattgcag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA03G39500.1 (Glycine max), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattg----tctttatcaatgcatgcaactagacatattattgttcacagtataataaa-ctgtaattttttcctgctacag------------------------------------------
|||| |||||||  |||||||||||||| ||||| ||||| || || ||||| || ||||| ||||||||||| |||||||||||||||||||| |||||||      |  ||      | |  ||| |   || ||      | | || || ||   | |   | |   |||    || || |    | ||                                          
CAAAACTTGTCCAGGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATAGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAGgtgtgaggaaaatcaggaatttagatctacctattcattatcccttctttttttttgtattgggaaagggctggttcttgtttcaataatagcagttttgcaaccttgtaatgtttttgggttgctgattgcag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G38030.1 (Glycine max), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtac-atttagcattgtctttatca-atgcatgcaactagacatattattgttcacagtataataaact--gtaattttttcctgctacag----------------------------
|||| ||||| ||||| |||||||| || ||||| || || || || ||||| |||||||| ||||||||||| ||||||||||| |||||||||||||||||  |  | |||     ||    | |    ||||| | ||| | || ||   | |  || |   |     ||||  | |    | | ||                             
CAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctggcaaaaaattagatatacatttgcaatt-gacttttttttcccccctctagagagactcaggtaaaatatagtggttccaaccttgatgtatcttgtggctgattgcag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA19G42110.1 (Glycine max), 5'ss of exon 4
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtac-atttagcattgtcttt-atcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgctacag---------------------------------------------
|||| |||||||| |||||||||||||| ||||| ||||| || || ||||| || ||||| ||||||||||| |||||||||||||||||||| ||||||||  |   ||||     ||  ||| | | || ||  ||    |  | || ||       |   |||  |    || ||  | | | |                                              
CAAAACTTGTCCGCGATGCCTTTCAGCTGGCAAAAGAGAAGTCTCCATGCATTATATTTATGGATGAAATTGATGCAATTGGAACAAAGCGTTTCGATAGgtatgagcaagcaggaatttagatctacgtattca-ttatcttttcttttctttttttattgggaaagggctggttcttgtttcaataatatcagttttgcaaccttgtgatgttatttggttgctggttgcag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgc---tacag
||||||||||||||||||||||||| ||||| || |||||| | || ||||| || || || |||||||| || || ||||| ||||||||||| || |||||||  |    || |  ||  |||| |||| |  |   ||  || |     |   |     |||    | | |||   ||    |||||
CAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTGGTACAAAGCGTTTCGACAGgtacaaatctttttctgatt-ccaattcatgtatttctgcactttctcagctat--ttgctcaaatcacattctttggttgagagtacag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctg--ctacag
|||| |||||||||||||| || | ||||||||| ||||||||||| || || || || || ||||| ||||||||||| || |||||||||||||||||||||           ||| | |  |  ||||  | ||   || ||||| |       || |  ||   | | ||||   ||   |||||
CAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAGGGACAAAGCGTTTTGATAGgtac-----------tctatctagagtcatgtca-taactattttattttctttctgatgactaatgctgacttttaattggcttacag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtaca----------tttagcattgtctttatca--atgcatgcaactagacatattattgttcacagtataa---taaact-gtaatt--ttttcctg-ctacag----------------------
| || |||||||||||||||||||||||||| || |||||||| || |||||||||||||| ||||||||||| || || || |||||||| ||||||||||| |          ||||||| |   | | |||  ||   |  | | | |   |||    || | | ||| |   | ||||  | |      | | || ||| ||                      
CGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAGGCACAAAGCGGTTTGATAGgtaaaccattattggtttagcactacatctttcatgatatttttatcaaaatggatttggattgaaattatcaaggtgaactcatgagcagcctccttgactatagacttttctgccttttattgcag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g01180.t01 (Vitis vinifera), 5'ss of exon 7
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgcaactagacatatt--------attgttcacagtataataaactgtaattttttcctgctacag----------------------------------------
|||| ||||| || ||||| || ||||||||||| ||||||||||| || |||||||| |||||||||||||| || ||||| || |||||||||||||||||  |   |   | ||||    |||   |    ||  ||| |||        ||   | || ||| ||  ||  |  | |  |   |  || |                                         
CAAAACTTGTTCGAGATGCATTCCAGCTTGCAAAAGAGAAATCCCCATGTATCATTTTCATTGATGAAATTGATGCCATTGGCACGAAGCGTTTTGATAGgtatctcgtgttctatctt-gcaaattagttgctctttacaaatttgacggagatgcattacggtacaaccaatggggagtgctgtttattaaaaagtgttcagtgattgttgttattgtgttattttactacag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgca-actagacatattattgttcacagtataataaactgtaattttttcctgctacag-------------------------------------------------------
|||| |||||  | || || || ||||| |||||||| ||| | ||||| ||||| || ||||||||| | || |||||||| || ||||||||||| ||||     | | | |||  |  |||| |  |  | ||   |||| || | |  |    |   |  ||  |||   || || || |  |                                                        
CAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTGGTACTAAGCGTTTTGACAGgt-----ttgtaatgttctcttcaaagtgtctatacagaacatcttgtagagcgtttttagaggaagggtacacttatcttggtcaaattgattatattatgacaatcttatttgtgacttgatcttcggtttatgttggcag

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ37626 (Selaginella moellendorffii), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgctacag
||||||| ||  | |||||||||||||| ||||| |||||  | |||||||||||||| || |||||| | ||||| ||||| || || |||||||||||||    || |  |         ||  ||  |       |||     ||    ||||                               
CAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTGGGACCAAACGTTTTGATAGgt----ttggtctcaaaacggacacggccggtttactaacagtgacttacatacag-------------------------------

upper sequence: LOC_Os02g56000.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ15061 (Selaginella moellendorffii), 5'ss of exon 6
CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttagcattgtctttatcaatgcatgcaactagacatattattgttcacagtataataaactgtaattttttcctgctacag
||||||| ||  | |||||||||||||| ||||| |||||  | |||||||||||||| || |||||| | ||||| ||||| || || |||||||||||||    || |   | ||   |   |  |  ||   |  ||  |   |   | ||| || |                           
CAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTGGGACCAAACGTTTTGATAGgt----ttgg---tctcaaaacggacaccggccggtttactaacagtgacttaca-tacag--------------------------

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|3759941|gb|C97199.1|C97199
EST:     TCATTTTTATTGATGAAATTNACGCAATTGGGACAAAGCGTTTTTGATAG                         TTAAGNTAGTGGTTACAGAGAAGT
genomic: TCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTT-GATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGT




















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: 55 (upstream exon), 75 (downstream exon)
Score: 40

CAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTGGAACAAAGCGTTTTGATAGgtacatttag ... cctgctacagTGAAGTTAGTGGTGACAGAGAAGTGCAGCGCACAATGTTGGAGTTGCTGAATCAGCTAGATGGATTCAGTAGTGACGAGAGGATAAAG




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