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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgtaattcacagttgaaaaataaaaataatctggaattgttgttttccaagataactcagttcattctattgatcttctggcag

Basic information

species Oryza sativa
transcript LOC_Os12g37870.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g37870.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G034083_T01 (Zea mays), 5'ss of exon 4
GTTCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgta---attcacagttgaaaaataaaaataatctggaattgttgttttccaagata----actcagttcat----tctattgatcttctggcag
|| || ||||| ||||||| |||||| |||| ||||| |||||||||||||||||   | ||    ||   |||   | | | | || | |||||| ||| | || |     |||||    |        |||| |  | | ||||
GTCCGCACAAAGATAGGTGGTTTCATTAGAGCTGTATTTTCTGTTTTCCAAGgtactcactcttgcttttcaaaggcagacagtttgtagttgttgcttttccagtttcaacactcaacataagatgctcattggttcttttgcag
















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|27577556|gb|CB000251.1|CB000251
EST:     TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAG                         ACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
genomic: TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgtaattcaca ... cttctggcagACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
EST: gi|33807858|gb|CF329821.1|CF329821
EST:     TCGGACAAAAATAGGTGACTTCATCAGAGGTGTATATTCTGTTTTCCAAG                         ACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
genomic: TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgtaattcaca ... cttctggcagACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
EST: gi|29669993|gb|CB666268.1|CB666268
EST:     TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAG                         ACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
genomic: TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgtaattcaca ... cttctggcagACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
EST: gi|58600487|gb|CK011015.1|CK011015
EST:     TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAG                         ACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
genomic: TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgtaattcaca ... cttctggcagACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
EST: gi|33800763|gb|CF326252.1|CF326252
EST:     TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAG                         ACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
genomic: TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgtaattcaca ... cttctggcagACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
EST: gi|58589196|gb|CF987504.1|CF987504
EST:     TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAG                         ACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG
genomic: TCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgtaattcaca ... cttctggcagACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGG

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: 52 (upstream exon), 66 (downstream exon)
Score: 28

GTTCGGACAAAAATAGGTGATTTCATCAGAGGTGTATATTCTGTTTTCCAAGgtaattcaca ... cttctggcagACTTGGATTTCTCATTCCTTGAGATGAATCCGTTCACCATGGTGAATGGGGAACCATATCCTCTAGACATGAGAGGAGAATTGGACGACACAGCTGCCTT




<











<


<