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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttattaatattaatcagaactagtatctttcgagggattcgtcgcattcctaatgatttgctacattgtatag

Basic information

species Oryza sativa
transcript LOC_Os12g07880.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07880.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G005848_T01 (Zea mays), 5'ss of exon 14
ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttattaatattaatcagaactagtatctttcgagggattcgtcgcattcctaatgatttgctacattgtatag--
 |||||||| ||||||| ||| |||||||||||||||||||||||||||||||| ||||| || || || | |    | || | |  ||  | |    |   |    |||| | | | | ||||||  |||| ||    
GTGTATGGAAGATTTGGAGAGTACCACTCGTTATGTCACTTGGTCCCTTCACAACAAGgtgcaatt-tttacacc--ttaggaattttaaatat----gtgctgtcagcatgcgtgacgttttgctttattggatgcag

upper sequence: LOC_Os12g07880.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA05G24890.1 (Glycine max), 5'ss of exon 10
ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttattaatattaatcagaactagtatctttcgagggattcgtcgcattcctaatgatttgctacattgtatag----------------------------------------------------------------------------------------------------------------------------
|||||||||||| |||||||||||||| || |||||  | ||| | || ||||||||||||  | | ||||     ||  | |     ||  ||   || || |  |   ||   | |   | ||| | |  | |                                                                                                                              
ATGTATGGAGGACTTGGTGAGCACCACACGGTATGTTTCATGGCCTCTCCACAATAAGgtattgat-ttaagggacatttgcagagacatgcttt--ggtatgctgcattttgaaagtatctcgctccctactttgaattttagctaggctcgtatgattatatccaccacttaagagcaaaagagtaatatattatttgctaagctaagttttcatggctcattttatatctcactctagtgtgactgtcaacattgtag

upper sequence: LOC_Os12g07880.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv12s0055g00490.t01 (Vitis vinifera), 5'ss of exon 14
ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttattaatattaatcagaactagtatctttcgagggattcgtcgcattcctaatgatttgctacattgtatag------------------------
||| ||||| || || ||||||||||| ||||||||||||||||| || |||||||||||    | |  |||   | |  |  || | |||      |  ||| |||   |   |   | | |  |   ||    |                         
ATGCATGGAAGACTTAGTGAGCACCACCCGTTATGTCACTTGGTCTCTCCACAATAAGgtt--ataagcaattccagtttgt-cttgcatcccatttgaaattggtctgttctgtttaggtctattctgttcagcatttgaaaggaaactggtatgtttaa

upper sequence: LOC_Os12g07880.1 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S304_66V6.2 (Physcomitrella patens), 5'ss of exon 16
ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttattaatat-------taatcagaactagtatctttcgagggattcgtcgcattcctaatgatttgctacattgtatag--------------
||||||||||||| |  |||||||||| || |||||||||||||| ||||| |||||||||   || || || |       ||  ||||     | |||| |||   | || |    ||| |     ||   |  |||  |                 
ATGTATGGAGGATCTAATGAGCACCACGCGGTATGTCACTTGGTCACTTCATAATAAGgtaatatttttcatgtatctgcttatgcagagactttctcttccgaatcactcattttgttcgtctatgttgattgtatttcagtccatttgtgtgtctt

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|88570954|gb|CI662327.1|CI662327
EST:     AGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG                         AACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAAG
genomic: AGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttat ... cattgtatagAACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAAG
EST: gi|88349832|gb|CI634367.1|CI634367
EST:     AGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCANAATAAG                         AACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAAGACCAA
genomic: AGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttat ... cattgtatagAACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAAGAGCAA
EST: gi|29629953|gb|CB634962.1|CB634962
EST:     AGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG                         AACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAAGAGCAA
genomic: AGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttat ... cattgtatagAACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAAGAGCAA
EST: gi|88326033|gb|CI651082.1|CI651082
EST:     AGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAG                         AACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAA
genomic: AGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttat ... cattgtatagAACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAA

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: 67 (upstream exon), 45 (downstream exon)
Score: 10

ATGTATGGAGGATTTGGTGAGCACCACTCGTTATGTCACTTGGTCCCTTCACAATAAGgtacagttat ... cattgtatagAACCGTGCCGGATTGAGACACTTCTTTGATTCCTTTGTTGCACAAGAGCAATTATCCGTGAACACACTTACTGCCCACTCGACTGGGCTGCATGAGCAAT




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