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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCAGTGAAGTTTTTGTTCACCAGTTGATCCACACAATTGAGTTTGTTCTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctagacattcagcatcaccgcattactttgaacagccttactccctcatcatcccacttttgatctataacaatgcactccttgttagccactaataatcgattaaattgtattctttatacag

Basic information

species Oryza sativa
transcript LOC_Os03g14690.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14690.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G058910_T01 (Zea mays), 5'ss of exon 16
AGTTCAGTGAAGTTTTTGTTCACCAGTTGATCCACACAATTGAGTTTGTTCTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctagacattcagcatcaccgcattactttgaacagccttactccctcatcatcccacttttgatctataacaatgcac-----tccttgttagc-cactaa----taatcgattaaattgtattctttatacag-----------------------------------
||||| |||||||||||||||||||  |||| ||||| || || |||||||| || ||||||||||| || || ||||| |||||||| |||||||| ||||| | |||    || ||||  | |   ||  |||  ||||||| ||     ||   |||||   ||  | | |     |||||     |||   |  |  || |       |  | |  || |  | || ||    ||                                    
AGTTCGGTGAAGTTTTTGTTCACCAACTGATTCACACGATAGAATTTGTTCTGGGTGCAGTCTCAAACACCGCTTCATACCTTCGTCTTTGGGCTCTGAGgtaatgcta--ttttaagcagtatc---tttatttacacagcctcacctatgcacagtcccatacttcctttgtttggctgcaccctaatccacataggtgcattggagtgcagccaaacaagtcattttattacctcactggctactaacgtgctactgatattctcctttcag

upper sequence: LOC_Os03g14690.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G104418_T02 (Zea mays), 5'ss of exon 7
AGTTCAGTGAAGTTTTTGTTCACCAGTTGATCCACACAATTGAGTTTGTTCTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctagacattcagcatcaccgcattactttgaacagccttactccctcatcatcccacttttgatctataacaatgca-ctccttgttagccactaataatcgattaaattgta----------ttctttatacag-----------------------------------------
||||||| |||||||||||||||||| |||| ||||| || || ||||||||||| ||||||||||| ||||| || || ||||| || |||||||| ||||| |  ||  | |  ||||| |   | ||| |||  ||||||| ||   | || |||||||   ||  |         ||   || |    ||  |   |   || ||||  | || |          || ||| || |                                          
AGTTCAGCGAAGTTTTTGTTCACCAGCTGATTCACACGATCGAATTTGTTCTTGGTGCAGTCTCAAACACAGCTTCGTACCTTCGCCTTTGGGCTCTGAGgtagtgtta--cttcaagcattatgtcttta-tttacacagcctcacctacacaacatcccatacttcctaagggcttgtgtggctgcaccctaatccacatggatagattggagtgcagccaaacaagttttttttataacttcaatggctactaacgagctactgatattctcccttcag

upper sequence: LOC_Os03g14690.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 5'ss of exon 16
AGTTCAGTGAAGTTTTTGTTCACCAGTTGATCCACACAATTGAGTTTGTTCTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctagacattcagcatcaccgcattactttgaacagccttactccctcatcatcccacttttgatctataacaatgcactccttgttagccactaataatcgattaaattgtattctttatacag----------------------------------------------------------------------
| ||||| ||| | ||||| |||||  | || ||||| ||||||||||| ||||| || || || || || || || |||||||||||||||||||||||||||    | | | |         |  ||     |||    | |  || ||  ||  ||| ||     | |||  ||    || |      |||| | || || ||  |||||||   |  ||  |   |                                                                      
AATTCAGCGAAATCTTTGTGCACCAACTCATTCACACCATTGAGTTTGTGCTTGGAGCTGTTTCCAACACTGCTTCTTATCTTCGTCTCTGGGCTCTCAGgtac---aaaatactacttgctttcaaatagtcctgattgtcat--ctaccagatagtcctacc--aaaactagcacttgtcaatatcatctagc-agtagtattctgttaaattcattggttcttgatggcttaatgtcgaagtattggtttgcgcatttcgtgactaatctttatgctttgctgggattcctattcag

upper sequence: LOC_Os03g14690.1 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv18s0001g13410.t01 (Vitis vinifera), 5'ss of exon 16
AGTTCAGTGAAGTTTTTGTTCACCAGTTGATCCACACAATTGAGTTTGTTCTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctagacattcagcatcaccgcattactttgaacagccttactccctcatcatcccacttttgatctataacaatgcactccttgttagccactaata-atcgattaaattgtattctttatacag
|||| |||||||||||||| |||||  | || || || || |||||||| ||||| |||||||| |||||||| |||||  | ||| | ||||| ||||||||       |||  | | |        ||| ||   |  || |          | | |  |  | ||  ||   | |||||| |  | |  |||||    ||  || ||  |||                
AGTTTAGTGAAGTTTTTGTACACCAACTTATTCATACCATAGAGTTTGTCCTTGGAGCAGTCTCTAATACAGCTTCATACTTACGTTTATGGGCCCTCAGgtaggcaggaacaacctgaa-------gttatttcatatggcatgc--------tgagctaaaatgtgcactgctaaaatgca-tggtagaaagccaaagttatgtctatagaata---------------

upper sequence: LOC_Os03g14690.1 (Oryza sativa), 5'ss of exon 16
lower sequence: PP1S296_62V6.1 (Physcomitrella patens), 5'ss of exon 15
AGTTCAGTGAAGTTTTTGTTCACCAGTTGATCCACACAATTGAGTTTGTTCTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttct---agacattcagcatcaccgcattac-tttgaacagccttactccctcatcatcccactt-ttgatctataacaatgcactccttgttagccactaataatcgat-taaattgtattctttatacag---------------------------
|||| |||||||||||||| |||||  |||| ||||| |||||||||||  |     | || || || || || || ||||| || || ||||| |||||||| ||||   ||   ||    || ||    || | |||  | || |||   |   |    |   || | ||||  |      |    || |     |     |    |||||  |   |  |  ||| |  || |                           
AGTTTAGTGAAGTTTTTGTGCACCAAATGATTCACACTATTGAGTTTGTGTTGAATTCTGTATCCAACACTGCTTCCTATCTGCGGCTGTGGGCGCTCAGgtaattctcttaggtgtt-gttattactttgttccatttagaaagtcttgtgctaactctttttaacgtgttgacgtggtgttaccagctgcaaaaaaattgttctgtatcgacatggttcatgctctctcgactgatcttttctaggacttttggcctgcag

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|87016370|gb|CI271781.1|CI271781
EST:     CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAG                         TCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
genomic: CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctag ... ctttatacagTCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
EST: gi|86477516|gb|CI120149.1|CI120149
EST:     CTGGGCTCTCAG                         TCGTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
genomic: CTGGGCTCTCAGgtacttctag ... ctttatacagTCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
EST: gi|29687308|gb|CB683583.1|CB683583
EST:     CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAG                         TCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
genomic: CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctag ... ctttatacagTCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
EST: gi|86481987|gb|CI124620.1|CI124620
EST:     CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAG                         TCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
genomic: CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctag ... ctttatacagTCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
EST: gi|86858351|gb|CI271192.1|CI271192
EST:     CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAG                         TCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
genomic: CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctag ... ctttatacagTCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
EST: gi|66916184|gb|CX103032.1|CX103032
EST:     CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAG                         TCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
genomic: CTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctag ... ctttatacagTCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
EST: gi|86827665|gb|CI272929.1|CI272929
EST:     CGTCTCTGGGCTCTCAG                         TCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT
genomic: CGTCTCTGGGCTCTCAGgtacttctag ... ctttatacagTCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCT

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: 71 (upstream exon), 60 (downstream exon)
Score: 20

AGTTCAGTGAAGTTTTTGTTCACCAGTTGATCCACACAATTGAGTTTGTTCTTGGGGCAGTCTCAAATACAGCCTCATATCTTCGTCTCTGGGCTCTCAGgtacttctag ... ctttatacagTCTTGCACACTCGGAGTTGTCAAGTGTATTCTATGACAAGGTTCTCCTCCTAGCTTTCGG




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