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

TGTGAACCTCCACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaattcggttactatattttttctgcttatgatggttaccttctaagcaatgtgttttgattttcag

Basic information

species Oryza sativa
transcript LOC_Os09g34910.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34910.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G164956_T02 (Zea mays), 5'ss of exon 9
TGTGAACCTCCACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaattcggttac-tatattttttc-------tgcttatgatggttaccttctaagcaatgtgttttgattttcag
||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||||| |   |||    | |  | |||||||         || |||| || | | |||  |||   |  |  ||||||||||||
TGTGAACCTCCCCGTGACGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatgctaaatattatcatgtttatttttgtatagtattgtttataattgcttcctgttaatgga-atcatttgattttcag

upper sequence: LOC_Os09g34910.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G149520_T02 (Zea mays), 5'ss of exon 9
TGTGAACCTCCACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaat-tcggttactatatttttt------ctgcttatgatggttaccttctaag-----caatgtgttt---tgattttcag-----------
||||||||||| || ||||||||||| ||||||||||||||||||||||| |||||||||||||     ||| |  | |  |   || | |      ||| |||| || | ||| |  |||      ||||  ||||   |||  || |            
TGTGAACCTCCCCGGGATGTTGAAGCTTACATACACCGGTCAGGTCGGACAGGGAGAGCAGgtatactaaatgttagatgtttgtttgtgtaaagtactgtttataattgctacatgttaatgcaatcaatacgtttaaatgacgtttaaactacatttaa
















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|4969173|gb|AU066077.1|AU066077
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|29672112|gb|CB668387.1|CB668387
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|218486017|gb|FG967018.1|FG967018
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|88336930|gb|CI627010.1|CI627010
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGT
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGT
EST: gi|87023726|gb|CI286477.1|CI286477
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|58686669|gb|CK075356.1|CK075356
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|218502440|gb|FG963347.1|FG963347
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|218487667|gb|FG948994.1|FG948994
EST:     ACGTGATGTTGAA-CCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|218495874|gb|FG947056.1|FG947056
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|29637932|gb|CB642941.1|CB642941
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
EST: gi|58691703|gb|CK080390.1|CK080390
EST:     ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAG                         GCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG
genomic: ACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATG

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: 61 (upstream exon), 75 (downstream exon)
Score: 44

TGTGAACCTCCACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaa ... tgattttcagGCAATACTGGTGTTGCTGTCATGCTTTTTGAACCCAGATATAAGTTCAATGTGAACAGAATAGAAAGGGAGTCTGGGGTCAAATTTGAACATATCTCTGC




<











<


<









Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTGAACCTCCACGTGATGTTGAAGCCTACATACACCGGTCAGGTCGGACTGGGAGAGCAGgtaggagtaattcggttactatattttttctgcttatgatggttaccttctaagcaatgtgttttgattttcag

- - - - - - - - -  TTGAAG
- - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG