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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGCGTTCTACGCCGCCTGCACTGCCGGTGGGATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttgggggaacgcctggatctgtgaccctgctggctttggcgcttctgggagccctgctccttcgtagatctggtgatatttagttttgttcgatg...

Basic information

species Oryza sativa
transcript LOC_Os02g52860.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 1
GCCGGCGTTCTACGCCGCCTGCACTGCCGGTGGGATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttgggggaacgcctggatctgtgaccctgctggctt-tggcgcttctgggagccctgctccttcgtagatctggtgatatttagttttgttcgatg---
|||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||  ||  | || ||| |||||||  ||| | ||       |    | |    |    | ||  | ||   |||  ||  |  | |      || | |   
GCCGGCCTTCTATGCCGCCTGCACTGCCGGAGGAATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCTCTCGACCTCGTCAAGTGCAATATGCAGgtgagcgggtagcac-cctagatctgtcgccccggtgctccacaggatctattttgggaaggttcactggt---tctaatggaacatggccagagtcaaagtca

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G060630_T01 (Zea mays), 5'ss of exon 1
GCCGGCGTTCTACGCCGCCTGCACTGCCGGTGGGATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttgggggaacgcctggatctgtgaccctgctggctttggcgcttctgggagccctgctccttcgtagatctggtgatatttagttttgttcgatg---
|||||| ||||| ||||||||||| | ||| || |||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||  |||     |||| |||||||| |||  | |   |   ||   ||           ||    |  |||||| || | ||| |||   |  || |   
GCCGGCCTTCTATGCCGCCTGCACCGTCGGAGGAATCGCCAGCTGCGGCCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAATGCAACATGCAGgtgagc-gggcagcggcctagatctgtgtcccc-cggtactccacgagcctttttttagaaatctcgtgcggatctg-tggtgtttggttggttgggaaggtt

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 1
GCCGGCGTTCTACGCCGCCTGCACTGCCGGTGGGATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttgggggaacgcctggatctgtgaccctgctggctttggcgcttctgggagccctgctccttcgtagatctggtgatatttagttttgttcgatg---
|||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||||||  ||  | || ||| |||||||  |||   ||        | | |     |    | | |   |    |||  ||  |  | |      || | |   
GCCGGCCTTCTATGCCGCCTGCACTGCCGGAGGAATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCTCTCGACCTCGTCAAGTGCAATATGCAGgtgagcgggtagcac-cctagatctgtcgcccctgtgctccacaggatccattttgggaagattcactg--attctaatggaacatggccagagtcaaagtca

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 1
GCCGGCGTTCTACGCCGCCTGCACTGCCGGTGGGATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttgggggaacgcctggatctgtgaccctgctggctttggcgcttctgggagccctgctccttcgtagatctggtgatatttagttttgttcgatg--
 || || ||||||||||||||||| |||||||| |||  |||||| || ||||| |||||||||||||| || || ||||| |||||||| || ||||||||    |          ||   ||| |     |       |       | |         | ||  || ||  | || | | |||||  | ||||   ||  
CCCTGCCTTCTACGCCGCCTGCACCGCCGGTGGAATCCTCAGCTGTGGCCTCACTCACATGGCCGTCACTCCTCTTGACCTAGTCAAGTGTAATATGCAGgttctctctctctctctctctctctctatatatatatatatatatatatatatatatatcgatctgtcttat-tgtgcttagatttaactctgtttt-tgtt

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 1
GCCGGCGTTCTACGCCGCCTGCACTGCCGGTGGGATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttgggggaacgcctggatctgtgaccctgctggctttggcgcttctgggagccc-tgctccttcgtagatctggtgatatttagttttgttcgatg
 || || ||||||||||||||||| |||||||| |||  |||||| || ||||| |||||| ||||||| || || ||||| |||||||| || ||||||||    |          ||   ||| |  | ||       |       | |         |     |   || || |    |||| ||  |   |  ||  
CCCCGCCTTCTACGCCGCCTGCACCGCCGGTGGAATCCTCAGCTGTGGCCTCACTCACATGACCGTCACTCCTCTTGACCTAGTCAAGTGTAATATGCAGgtcctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatatatatatatatatatatatcgatctgac-

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|58611247|gb|CK038959.1|CK038959
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|58654180|gb|CK042860.1|CK042860
EST:     TCACCCACATGGCCGTCACGCCGCTGGGGCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|88335400|gb|CI650365.1|CI650365
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|29677043|gb|CB673318.1|CB673318
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|58656567|gb|CK045247.1|CK045247
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|58690463|gb|CK079150.1|CK079150
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|88327873|gb|CI648271.1|CI648271
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGG
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGG
EST: gi|88302330|gb|CI668176.1|CI668176
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|66913316|gb|CX100164.1|CX100164
EST:     TCACCCACATGGCCGTCACGCCGGTCGACCTAGTCAAGTGCGACATGCAG                         ATTGATCCTGCATTGTACAATAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|3761935|gb|C99183.1|C99183
EST:     CCCACATGGGCCGTCACGCCGCTCGACCTTCGTCAANTGGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: CCCACATGG-CCGTCACGCCGCTCGACCT-CGTCAAGTG-CAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|58657826|gb|CK046506.1|CK046506
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|58587321|gb|CF985629.1|CF985629
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|29630079|gb|CB635088.1|CB635088
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|88389403|gb|CI600572.1|CI600572
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATA-AAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|58657558|gb|CK046238.1|CK046238
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|29658501|gb|CB654776.1|CB654776
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACACCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|58683632|gb|CK072319.1|CK072319
EST:     TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|42592172|gb|CK738658.1|CK738658
EST:     GCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: GCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
EST: gi|58664392|gb|CK053078.1|CK053078
EST:     TCACCCACATTGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA
genomic: TCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTA

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: 75 (upstream exon), 72 (downstream exon)
Score: 69

GCCGGCGTTCTACGCCGCCTGCACTGCCGGTGGGATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttggg ... tttttttcagATTGATCCAGCAAAATACAAGAGCATAACATCTGGGTTTGGCGTCCTCTTAAAGGAGCAAGGACCTAGAGGCTTCTTCAGGGGATGGGTGCCTACCTTGC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGGCGTTCTACGCCGCCTGCACTGCCGGTGGGATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtgagttgggggaacgcctggatctgtgaccctgctggctttggcgcttctgggagccctgctccttcgtagatctggtgatatttagttttgttcgatg

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttc