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

TCCAACTGGCTCTGATTTTTGCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAGgttctgttttttaacttggtgatccagcattggttggaagcaagcttagcgccattaaatttcatggtatctttatgcaagatgtgtgcttatatgctttccaactcttacagttgaattgcaaaacttccatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g37770.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37770.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G015364_T02 (Zea mays), 5'ss of exon 5
TCCAACTGGCTCTGATTTTTGCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAGgttctgttttttaacttggtgatccagcattggttggaagcaagcttagcgccattaaatttcatggtatctttatgcaagatgtgtgcttatatgctttccaactcttacagttgaattgcaaaacttccatgcag
| |||||||| ||||||||||| ||||| || || || || ||||| |||||| |  |||||||||||||||||||   || || |       | ||  ||||||       |  | |  |  |||   | |||| | ||      |  || ||  |||| ||    | || || ||||     || |||| ||||  |  ||||||
TTCAACTGGCCCTGATTTTTGCGCACACTGAGAAGTACCCTGATGAACCTCCGGTACTGAATGTCAAAAGgttctgccattaaatt-------ctagttttggtt-----tcatttcatagttattt--tgtcataggat------gtgagctgaatgctgat----tgtctaattctt-----tggattggaaaatatttatgcag
















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|218501991|gb|FG959119.1|FG959119
EST:     GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAG                         TGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAACGAAAAGCTTGA
genomic: GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAGgttctgtttt ... ttccatgcagTGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA
EST: gi|29670377|gb|CB666652.1|CB666652
EST:     TTGAATGTCAAAAG                         TGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA
genomic: TTGAATGTCAAAAGgttctgtttt ... ttccatgcagTGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA
EST: gi|66913764|gb|CX100612.1|CX100612
EST:     GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAG                         TGTACGAGGAATGAAATCAGAAGATCTT
genomic: GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAGgttctgtttt ... ttccatgcagTGTACGAGGAATGAAATCAGAAGATCTT
EST: gi|29670376|gb|CB666651.1|CB666651
EST:     GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAG                         TGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA
genomic: GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAGgttctgtttt ... ttccatgcagTGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA
EST: gi|32948343|gb|BP184915.1|BP184915
EST:     GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTATGAATGTCAAAAG                         TGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA
genomic: GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAGgttctgtttt ... ttccatgcagTGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA
EST: gi|88456108|gb|CI567674.1|CI567674
EST:     GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAG                         TGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA
genomic: GCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAGgttctgtttt ... ttccatgcagTGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGA

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), 58 (downstream exon)
Score: 39

TCCAACTGGCTCTGATTTTTGCACACACCGAAAAATATCCGGATGAGCCTCCGCTTTTGAATGTCAAAAGgttctgtttt ... ttccatgcagTGTACGAGGAATGAAATCAGAAGATCTTGCATCCTTGAAAGAAAAGCTTGAGCAAGAG




<











<


<