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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCTTATAGCCAAAAGTTTATCTACTTCTGAGCAGCAAGATGCATCAGGAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaacacttaattttgcttctgaattcaggtctgctgctcttgttaatataggtaactaaaacactaagcaattcccactgaaaactgtgatga...

Basic information

species Oryza sativa
transcript LOC_Os05g44922.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44922.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G004932_T01 (Zea mays), 5'ss of exon 11
GGATCTTATAGCCAAAAGTTTATCTACTTCTGAGCAGCAAGATGCATCAGGAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaa---acacttaa-----ttttgcttctgaattcaggtctgctgctct-tgttaatataggtaactaaaacactaagcaattcccactgaaaactgtgatga--------------------------------------------------------------
||||||||| || ||||||||| | || || || || |||||||| || ||||||||||| || ||||||||||||||||||||||||||||||||||||||||| ||    | |  |||     | ||||| ||| |||   | |   |    | ||||    |  |  | | |    ||  |  ||| | | |||      ||                                                                  
GGATCTTATCGCGAAAAGTTTAGCCACATCAGATCAACAAGATGCGTCTGGAAATAAGCTGCTTCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacataactatataactaaaatattcttgctgctggatttgagccacttatcttatgttgtagtttggtattcactgtctcgggtattgcaaatgagctaaatggctccactatactgtatgtggttcttgaaagttttgcttaataggccttgtgctaattcctcgtag
















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|4716362|gb|AU057478.1|AU057478
EST:     GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
genomic: GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
EST: gi|27578240|gb|CB000935.1|CB000935
EST:     GCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
genomic: GCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
EST: gi|58679575|gb|CK068262.1|CK068262
EST:     GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
genomic: GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
EST: gi|56157880|gb|C27510.2|C27510
EST:     GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
genomic: GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
EST: gi|2310958|gb|C27113.1|C27113
EST:     GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACCACTTCA-GAGCAAAA-GATGGAGATN-CTATTAAATATATAGA
genomic: GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAGA
EST: gi|27576923|gb|CA999617.1|CA999617
EST:     GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
genomic: GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
EST: gi|27578068|gb|CB000763.1|CB000763
EST:     CTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
genomic: CTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
EST: gi|27576260|gb|CA998954.1|CA998954
EST:     GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAG                         GACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG
genomic: GAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG

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: 73 (upstream exon), 46 (downstream exon)
Score: 34

GGATCTTATAGCCAAAAGTTTATCTACTTCTGAGCAGCAAGATGCATCAGGAAATAAGCTACTGCTTGATATTGGTCTTTGGCTGACTCACAAGATAAAGgtacacaaaa ... tctattgtagGACCACTTCAAGAGCAAAAAGATGGAGATGACTATTAAATATATAG




<











<


<