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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTTGGGTCCAGTTTAACTCTGACTGGAGTCGTTTGTTAGTAGTACATGAGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatatatgctgtatcaaaaatggatagaattcctatgttcataattgatcaaataattttgttctggtttgctaaaatctcttttttatctctcttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os01g15020.2
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G416836_T01 (Zea mays), 5'ss of exon 21
TACTTGGGTCCAGTTTAACTCTGACTGGAGTCGTTTGTTAGTAGTACATGAGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagc-tat-atatgctgtatcaaaaatggatagaattcctatgttc-ataattgatcaaataattttgttctggtttgctaaaatctcttttttatctctcttgtttcag
|||  ||||||||||||  ||||||   | ||  ||| |||||||||| |||||||| ||||| ||||||||||||||||||||||| || ||||| ||||| ||  || |||| ||  ||||||||    ||   |  |  ||    || |   || |||||  ||| |  || ||                                  
TACACGGGTCCAGTTTAGTTCTGACCAAAATCACTTGCTAGTAGTACAAGAGACTCAACTAGCCATATATGATGCATCAAAAATGGAGAGGATCTATCAGgttgcacatcatatactagatcaaaaagtactattttctcattgcctgattacctattaaatatgtttatcttgtttcag-------------------------------
















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|86597087|gb|CI272682.1|CI272682
EST:     CTCAGCTAGCTATATATGATGCATCGAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: CTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|87020791|gb|CI269508.1|CI269508
EST:     TATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: TATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|29630394|gb|CB635403.1|CB635403
EST:     AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTCCCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|86860682|gb|CI324949.1|CI324949
EST:     AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|58680385|gb|CK069072.1|CK069072
EST:     AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|86477786|gb|CI120419.1|CI120419
EST:     AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|33795487|gb|CF323613.1|CF323613
EST:     AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|88828342|gb|CI000451.1|CI000451
EST:     AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|24208900|gb|AU225927.1|AU225927
EST:     AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTT
genomic: AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTT
EST: gi|29626132|gb|CB631143.1|CB631143
EST:     AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: AGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|86482317|gb|CI124950.1|CI124950
EST:     TCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: TCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
EST: gi|29630453|gb|CB635462.1|CB635462
EST:     GCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAG                         TGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA
genomic: GCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCA

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), 74 (downstream exon)
Score: 73

TACTTGGGTCCAGTTTAACTCTGACTGGAGTCGTTTGTTAGTAGTACATGAGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatat ... cttgtttcagTGGATACCTCAGGACGCTTTGTCAGCTCCCATTTCACATGCATCATACTCACGCAACAGCCAGTTGGTTTTTGCTGCCTTTACCGATGGTAACATAGGAA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTTGGGTCCAGTTTAACTCTGACTGGAGTCGTTTGTTAGTAGTACATGAGACTCAGCTAGCTATATATGATGCATCAAAAATGGAAAGAATCTACCAGgtagctatatatgctgtatcaaaaatggatagaattcctatgttcataattgatcaaataattttgttctggtttgctaaaatctcttttttatctctcttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA