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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacctagcacgattttaattcatttaatttaattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g13870.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G041980_T05 (Zea mays), 5'ss of exon 2
--------------------------------GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacctagcacgattttaattcatttaatt--taattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcag
                                ||| ||| | |||||||| ||||||||||||||| ||||| |||||| ||| ||||||||||||||||||||||||||||||||||| |||||| |||| |||||     |    | |||||  ||  |||  ||  |  || ||  ||   |   |   | | |  ||                                                                                                                    
TTCGGCGGCCGGCACGAGCACTTCCCCGGCACGCTGCCCACGGGCTCCGAGGTGCAGTCGCTCGTCATCGAGATCATCACCACATTCTACCTCATGTTCGtcatctccggcgtcgccacggacaacagagcagtaagtcgt-tgttgccattttg-tttgtttgtttgtttgtttctttcttttccggtcgttcaacccgta-------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os02g13870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G041980_T06 (Zea mays), 5'ss of exon 2
GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacctagcacgattttaattcatttaatt--taattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcag
||| ||| | |||||||| ||||||||||||||| ||||| |||||| ||| ||||||||||||||||||||||||||||||||||| |||||| |||| |||||     |    | |||||  ||  |||  ||  |  || ||  ||   |   |   | | |  ||       ||   ||||||| || |                                                                                            
GCTGCCCACGGGCTCCGAGGTGCAGTCGCTCGTCATCGAGATCATCACCACATTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACGGACAACAGAGCAgtaagtcgt-tgttgccattttg-tttgtttgtttgtttgtttctttcttttccggtcgttcaacccgtacgtactgtgcatatatatttgcag-------------------------------------------------------------------------------------------

upper sequence: LOC_Os02g13870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA15G09370.1 (Glycine max), 5'ss of exon 4
GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacctagcacgattttaattcatttaatttaattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcag
 ||||| | ||| || ||| |||| ||  | ||  |||| ||||| ||||| || || |||||||||||||| || ||||| |||||||| ||| |||| |||| ||  |  |     || |  ||||    |   ||   ||  ||    |||| |    | |    ||||| || | |  | || |  |||||      |                                                                                 
ACTCCCTGGCGGTTCTGACTTGCAATCTTTTGTGGTCGAATTCATAATCACTTTTTATCTCATGTTCGTCATTTCTGGCGTTGCCACCGATAACAGAGCGgtaatctttcctg-----ttcttgttcaaaagaaagaaaaacttgcttttttaatgatgggtgtgtcctaatttgtgt-tgaacattttgaatttagcaaataggg-----------------------------------------------------------------------------

upper sequence: LOC_Os02g13870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv14s0006g01540.t01 (Vitis vinifera), 5'ss of exon 3
GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacctagcacgattttaattcatttaatttaattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcag
  | || ||||| ||  | |  |||||  | ||||| ||  ||||||||||||||   ||||||||||||||||||||||| |||||||| |   ||||     | || | |  ||    |   ||| ||  || ||  |  |   ||   ||  |||  |  ||  ||     ||||   | | | | |  | ||                                                                                       
TGTTCCTGCCGGATCTCATGGCCAGTCTTTAGTCCTTGAAATCATCATCACCTTCCTACTCATGTTCGTCATCTCCGGCGTTGCCACCGATAGTAGAGC-----Ggtatccaataca--ctcgcttctttcgatgtacattgttaatctattatctaacaacttaagttttaaggttttagtcttttttttttatgcag------------------------------------------------------------------------------------

upper sequence: LOC_Os02g13870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv10s0003g01830.t01 (Vitis vinifera), 5'ss of exon 3
GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacctagcacgattttaattcatttaatttaattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcag
 || || || ||||| ||| |||||||  | ||| |||||||||| ||||| |||||||||||||| |||||||||||||| |||||||||||  |||| ||| | |   ||| ||    ||||    || |  || ||   | ||     |  |||     ||  |    ||   |||  ||  ||   || ||  ||   | ||| |                                                                          
TCTTCCGGCAGGCTCGGACTTGCAGTCCTTTGTCATCGAGTTCATAATCACATTCTACCTCATGTTTGTCATCTCCGGCGTTGCCACCGACAATAGAGCTgtatgat-tgtagtac----ttaacctcttca--ttcatgaattccaaaagtttttatcctacttctcctctttcattcattaattccaaaagtt--ttatcctactta--------------------------------------------------------------------------

upper sequence: LOC_Os02g13870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ36013 (Selaginella moellendorffii), 5'ss of exon 3
GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacctagcacgattttaattcatttaatttaattgctccctccgctaattaattatctagtttaattagtttctatatatctgtaatttgattgctccactaattaggatcgatttgatcctgattaatctgaaagttttgaagtgataattctgttgaccatatgcatggatgcag
  | ||||| ||   |||  | |||||| ||   || ||    |||||||||| |   |||||||||||| |||||| |||||||||||||   ||||| ||||||  |    ||   | |   |  ||     |  | ||  | |  || |  |  |                                                                                                                             
AATTCCCGCTGGAAGCGATCTCCAGTCGTTCTATCTGGAAGCGATCATCACCTACATTCTCATGTTCGTCGTCTCCGCCGTCGCCACCGACGCTCGAGCGgtaagcgccgacacatcctctctgtagatgccgctctaatgtccgcgacgatcgtgtag----------------------------------------------------------------------------------------------------------------------------

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|27576099|gb|CA998793.1|CA998793
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|29645400|gb|CB650407.1|CB650407
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|3762322|gb|C99570.1|C99570
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|33676006|gb|CF304245.1|CF304245
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|87018417|gb|CI252171.1|CI252171
EST:     GTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: GTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|33674773|gb|CF303012.1|CF303012
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|11025684|gb|AU162285.1|AU162285
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|33676643|gb|CF304882.1|CF304882
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|8251174|gb|AU091321.1|AU091321
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|5851059|gb|AU078231.1|AU078231
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|29645154|gb|CB650161.1|CB650161
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|29645401|gb|CB650408.1|CB650408
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|86506102|gb|CI148735.1|CI148735
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
EST: gi|88962440|gb|CI097592.1|CI097592
EST:     CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCC                         ATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG
genomic: CCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTG

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: 62 (upstream exon), 73 (downstream exon)
Score: 23

GCTCCCCGCCGGCTCCGACGTGCAGTCGCTCGTCCTCGAGTTCATCATCACCTTCTACCTCATGTTCGTCATCTCCGGCGTCGCCACCGACAACCGAGCCgtaagctacc ... atggatgcagATCGGGGAGCTGGCAGGGCTGGCCGTTGGTGCAACCATCCTGCTTAACGTGCTGATTGCTGG




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