Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCGAAGTTCTCTCAAGTTAAAAGAAATCATGAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgtacaacaactgcattttctctgttacactcaatttagttggtcacattatctttagttattcgttggcatatgaaatgcagctgcatttatgtctacca...

Basic information

species Oryza sativa
transcript LOC_Os07g40510.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g40510.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G414002_T02 (Zea mays), 5'ss of exon 10
ATTCGAAGTTCTCTCAAGTTAAAAGAAATCATGAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgta-caacaa-ctgcattttctctgttacactcaatttagttggtcacattatctttagttattcgttggcatatgaaatgcagc-tgcatttatgtctacca
|| |||| |||||||||||| |||||||| ||||||||||| || |||||||| |||||  |||||||||| ||||||||||||| ||| ||  ||  | || | | |  |   || ||| ||  |   || | |  ||    |   | | |  ||     | |    ||||  |   |  |  |
ATCCGAACTTCTCTCAAGTTGAAAGAAATAATGAAGAAAATCCTTCTCCTTGGAAATACTCTGAACCAGGGAACTGCTAGAGgtaacaataaattggctcttttgtttgccgtccagttttgtcag---cagtttgattgacaacaagatagtgtaactctttctttgtgcagcttgtttcaata

upper sequence: LOC_Os07g40510.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G132810_T01 (Zea mays), 5'ss of exon 2
ATTCGAAGTTCTCTCAAGTTAAAAGAAATCATGAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgta-caacaa-ctgcattttctctgttacactcaatttagttggtcacattatctttagttat-tcgttggcatatgaaatgcagctgcatttatgtctacca
|| |||| |||||||||||| |||||||| ||||||||||| || ||||||||||||||  |||||||||| ||||||||||||| ||| ||  ||| | || | | |  |   || ||| ||        | ||   ||   || ||||       |    |   |||  ||  |     |   
ATCCGAACTTCTCTCAAGTTGAAAGAAATAATGAAGAAAATCCTTCTCCTTGGGAATACCCTGAACCAGGGAACTGCTAGAGgtaacaataaattgcttcttttgtttgtcgtccagttttgtctacagtttgattgataacaatatcgtgtaagcctttctttgtgcttaatacacaaaaa---

upper sequence: LOC_Os07g40510.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 5'ss of exon 13
ATTCGAAGTTCTCTCAAGTTAAAAGAAATCATGAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgtacaacaactgcatt-ttctctgttacactcaatttagttggtcacattatctttagttattcgttggcatatgaaatgcagctgcatttatgtctacca
 |||| | |||  | || || || ||||||||||||||||||||   ||| ||||||||||||||||| || ||||| || |||  |  |  | |||  || | |   | |   |||||  ||        ||  ||  |  ||        || | |        ||| || | ||      
GTTCGCAATTCGGTGAAATTGAAGGAAATCATGAAGAAAATTCTTTACCTCGGGAATACATTGAACCAAGGAACTGCAAGGGgtg-aggactttcatagttatttagaagatctaattttattccagctgctactttagggcatatacaaagattttattctatcttgccttaaggtgaggtt

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|396941169|gb|HO188378.1|HO188378
EST:     AAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGGCTAGAG                         GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACC
genomic: AAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACT-GCTAGAGgtacaacaac ... ttgcttacagGTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACC
EST: gi|88329532|gb|CI648594.1|CI648594
EST:     GAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGGTAGAG                         GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCC
genomic: GAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgtacaacaac ... ttgcttacagGTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCC
EST: gi|29631359|gb|CB636368.1|CB636368
EST:     GAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAG                         GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTNAAACTCACAGATACCC
genomic: GAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgtacaacaac ... ttgcttacagGTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCC
EST: gi|29631370|gb|CB636379.1|CB636379
EST:     GAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAG                         GTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCC
genomic: GAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgtacaacaac ... ttgcttacagGTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCC

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: 72 (upstream exon), 60 (downstream exon)
Score: 13

ATTCGAAGTTCTCTCAAGTTAAAAGAAATCATGAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgtacaacaac ... ttgcttacagGTGCTGCAGTTGGCTTCCGGTTGGACAGTCTTCTAAAACTAACAGATACCCGAGCAACAAATAATAAAATGACACTTATGCACTACCTCTGCAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCGAAGTTCTCTCAAGTTAAAAGAAATCATGAAGAAAATTCTCCTCCTTGGGAATACATTGAACCAGGGTACTGCTAGAGgtacaacaactgcattttctctgttacactcaatttagttggtcacattatctttagttattcgttggcatatgaaatgcagctgcatttatgtctacca

- - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - CTCCTC