Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctgattcctagtatttccattgttttttttccaccttagtcattatcagctgtgctgtgtttatttgactgctcaagacatacaaccgctgagcttgccataacccttgatgctaagcttgttgataacaaattcattgcttgtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGATGGACTTGAGGCCTCTGGTTTGAGTGACCTATCCCGAGTGACCAGTGTAG

Basic information

species Oryza sativa
transcript LOC_Os01g70170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70170.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G134256_T01 (Zea mays), 3'ss of exon 3
gtaagtcctgattcctagtatttccattgttttttttccaccttagtcattatcagctgtgctgtgtttatttgactgctcaagacatacaaccgctgagcttgcca---taacccttgatgctaagcttgttgataacaaattcattgct------tgtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGATGGACTTGAGGCCTCTGGTTTGAGTGACCTATCCCGAGTGACCAGTGTAG
                                                  ||   |||| | | ||  |     ||||||        |     | ||| || |  |   ||||   |  || |||| || ||| | ||| |||| ||| |      |||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| | ||||| || ||||| ||||| ||||||||| |||||||||| || || || |
-------------------------------------------------gtaattgctgagttctgcattgcccactgctttcatatgattgtggttgaactcgatagtgtaactgcttgtggtaagattattgttcacatattcgttggtcgttgctgtcgctgcagCTTATTTTCTCAATTGCAAGATATGAGGCTGTGATTGATGCTTACCTCGATGGGCTAGAGGCTTCTGGCTTGAGTGACTTATCCCGAGTTACTAGCGTTG
















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|58586837|gb|CF985145.1|CF985145
EST:     TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACA                         CTTATCTTCTCGATTGCGAGATACGAGGCTGTGATTGATGCTTACATTGAT
genomic: TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
EST: gi|27554160|gb|CA998060.1|CA998060
EST:     TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACA                         CTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
genomic: TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
EST: gi|5005432|gb|AU070594.1|AU070594
EST:     TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACA                         CTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
genomic: TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
EST: gi|58611405|gb|CK039117.1|CK039117
EST:     TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACA                         CTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
genomic: TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
EST: gi|38476332|gb|CF960465.1|CF960465
EST:     TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACA                         CTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
genomic: TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
EST: gi|29688089|gb|CB684364.1|CB684364
EST:     TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACA                         CTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
genomic: TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
EST: gi|33693591|gb|CF321830.1|CF321830
EST:     TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACA                         CTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
genomic: TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
EST: gi|88745334|gb|CI768694.1|CI768694
EST:     TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACA                         CTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT
genomic: TTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGAT

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: 74 (upstream exon), 73 (downstream exon)
Score: 83

GGTCGACAGGCCCAATGTCTACATAAAGATCCCTGCTACCGCAGAATGTGTTCCTTCTATCAAGGAAGTTATTGCTAATGGCATTAGTGTCAACGTCACAgtaagtcctg ... gtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGATGGACTTGAGGCCTCTGGTTTGAGTGACCTATCCCGAGTGACCAGTGTAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccataacccttgatgctaagcttgttgataacaaattcattgcttgtcgctgcagCTTATCTTCTCGATTGCAAGATACGAGGCTGTGATTGATGCTTACATTGATGGACTTGAGGCCTCTGGTTTGAGTGACCTATCCCGAGTGACCAGTGTAG
                         tgataac  putative branch site (score: 83)
                           ataacaaattcatt  TA-rich tract