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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTCCGAGTCGACCCTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAGgtatgtctgtccgtagcttcttaaacttctaagtatttctggcagctttcttgtgttgatttatgcttgacttgtgctttgggacatgtttagctagggt...

Basic information

species Oryza sativa
transcript LOC_Os03g55490.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g55490.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G007399_T01 (Zea mays), 5'ss of exon 2
ATATTCCGAGTCGACCCTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAGgtatgtctgtccgtagcttcttaaacttctaa-gtatttctggca-gctttcttgtgttgatttatgcttgacttgtgctttgggacatgtttagctagggt--------
||||||||||| ||||||||||||| ||| |||||||| || || |||||||| |||||  | ||||||||| ||     |||| ||     ||  || ||  |     |  | |||| | ||    || ||      || |||||||        |   || | |||        
ATATTCCGAGTGGACCCTTTCTTTAGTGGCCAGGATAATTATGATCAATTAGTGAAAATAGCTGAGgtatgtttga----agctgctctgtgttgaaacgtcctgtcatcgtgttttcctatgccacttaat------ctagtgctttaaatggcataatgcaatggttgcaagtc
















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|58030601|gb|CX728144.1|CX728144
EST:     CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAG                         GTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAG
genomic: CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAGgtatgtctgt ... attatcgtagGTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAG
EST: gi|29644831|gb|CB649838.1|CB649838
EST:     CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAG                         GTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAG
genomic: CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAGgtatgtctgt ... attatcgtagGTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAG
EST: gi|29643382|gb|CB648389.1|CB648389
EST:     CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAG                         GTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAG
genomic: CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAGgtatgtctgt ... attatcgtagGTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAG
EST: gi|66915335|gb|CX102183.1|CX102183
EST:     CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAG                         GTTCTTGGAACAGAAGATTTCTACAACTTACCTTGGAAAAGTATGGTCTTG
genomic: CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAGgtatgtctgt ... attatcgtagGTTCTTGGAACAGAAGATTTCTACAA-TTACCTT-GAAAAGTATGGTCTTG
EST: gi|86595025|gb|CI260264.1|CI260264
EST:     CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAG                         GTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAG
genomic: CTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAGgtatgtctgt ... attatcgtagGTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAG

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: 62 (upstream exon), 55 (downstream exon)
Score: 8

ATATTCCGAGTCGACCCTTTCTTTAATGGTCAGGATAACTACGACCAATTAGTCAAAATTACCGAGgtatgtctgt ... attatcgtagGTTCTTGGAACAGAAGATTTCTACAATTACCTTGAAAAGTATGGTCTTGAGCTTGACCCGCAGCTTGAAAGACTTGTTGGAAG




<











<


<