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

gtatgccttcttgttttacttgatctatctgtgggttccattattcaaatgtttgattgctctgcttacatgatcttctttgccttttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTTGAGACGATCAATTCTATTTCTGAGTCTGAGAACATATACGATGTGACCA

Basic information

species Oryza sativa
transcript LOC_Os09g17850.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g17850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G400092_T01 (Zea mays), 3'ss of exon 8
gtatgccttc-ttgttttacttgatctatctgtgggttccattattcaaa------tgtttgattgctc---tgcttacatgatcttctttgccttttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTTGAGACGATCAATTCTATTTCTGAGTCTGAGAACATATACGATGTGACCA
 ||  |   | ||| |  | |||   || |  ||  ||     | | |||      | | |   ||      || ||| ||||| || || |  |||| ||||||||| || |||||||||||||| |||||||||||||| ||| ||||||||||  | ||||||| |||| |  ||||||||||||| |||||||| || |
ttaaactgacattgatagagttg-cataaccatgcattttggaaattaaagcacgatttctatctggctaggtgtttatatgattttgtt-gtatttt-tcagATACTTGTGTTGCCACCTTATCAGGGTGAAGGCCATGGTCTTGGTCTTCTTGAAGCAATCAATTATATTGCACAGTCTGAGAACATTTACGATGTTACAA

upper sequence: LOC_Os09g17850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G135966_T01 (Zea mays), 3'ss of exon 3
-gtatgccttc-ttgttttacttgatctatctgtgggttccattattcaaa------tgtttgattgctc---tgcttacatgatcttctttgccttttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTTGAGACGATCAATTCTATTTCTGAGTCTGAGAACATATACGATGTGACCA
  ||  |   | ||| |  | |||   || |  |   ||     | | |||      | | ||  ||      || ||| ||||| |  |   |  ||| ||||||||| || |||||||||||||| |||||||||||||| ||| ||||||||||  | ||||||| |||| |  ||||||||||||| |||||||| || |
gttaaactgacattgatagagttg-cataaccatacattttggaaattaaagcacgctttctgtctggctaggtgtttatatgatttagt---caatttttcagATACTTGTGTTGCCACCTTATCAGGGTGAAGGCCATGGTCTTGGTCTTCTTGAAGCAATCAATTATATTGCACAGTCTGAGAACATTTACGATGTTACAA

upper sequence: LOC_Os09g17850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G851405_T01 (Zea mays), 3'ss of exon 8
----------gtatgccttcttgttttacttgatctatctgtgggttccattattcaaatgtttgattgctctgcttacatgatcttctttgccttttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTTGAGACGATCAATTCTATTTCTGAGTCTGAGAACATATACGATGTGACCA
           |   |    |||  | ||   || | |  |   ||             ||| ||  |    || ||| | ||| || || |  |||| ||||||||| || |||||||||||||| |||||||||||||| ||| ||||||||||  | ||||||| |||| |  ||||||||||||| |||||||| || |
ttaaactgacattgacagagttgcataaccatatattttggaaagtaaagcacactttctgtctgtctagg-tgtttatacgattttgtt-gtatttt-tcagATACTTGTGTTGCCACCTTATCAGGGTGAAGGCCATGGTCTTGGTCTTCTTGAAGCAATCAATTATATTGCACAGTCTGAGAACATTTACGATGTTACAA

upper sequence: LOC_Os09g17850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G448927_T01 (Zea mays), 3'ss of exon 9
gtatgccttc-ttgttttacttgatctatctgtgggttccattattcaaa------tgtttgattgctc---tgcttacatgatcttctttgccttttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTTGAGACGATCAATTCTATTTCTGAGTCTGAGAACATATACGATGTGACCA
 ||  |   | |||    | |||   || |  |   ||     | | |||      | | ||  ||      || ||| ||||| || || |  |||| ||||||||| || |||||||||||||| ||||||||| |||| ||| ||||||||||  | ||||||| |||| |  ||||| ||||||| |||||||| || |
ttaaactgacattgacagagttg-cataaccatacattttggaaattaaagcacactttctgtctggctaggtgtttatatgattttgtt-gtatttt-tcagATACTTGTGTTGCCACCTTATCAGGGTGAAGGCTATGGTCTTGGTCTTCTTGAAGCAATCAATTATATTGCACAGTCTAAGAACATTTACGATGTTACAA

upper sequence: LOC_Os09g17850.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G106640_T01 (Zea mays), 3'ss of exon 3
-gtatgccttc-ttgttttacttgatctatctgtgggttccattattcaaatgtttgattgctctgcttacatgatctt----ctttgcct-tttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTTGAGACGATCAATTCTATTTCTGAGTCTGAGAACATATACGATGTGACCA
  ||  |   | ||| |  | |||    | |      ||     ||| ||        |   ||||  ||  || |  |     || | |  ||| ||||||||| || |||||||||||||| |||||||||||||| ||| ||||||||||  | ||||||| |||| |  ||||| ||||||| |||||||| || |
gttaaactgacattgatagagttgcataaccatacattttggaaattaaagcacgctttctgtctggctaggtgtttatacgatttagtcaatttttcagATACTTGTGTTGCCACCTTATCAGGGTGAAGGCCATGGTCTTGGTCTTCTTGAAGCAATCAATTATATTGCACAGTCTAAGAACATTTACGATGTTACAA

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|218500852|gb|FG953841.1|FG953841
EST:     TTCATCATTTTTATCACTACCCTGAGAGCACTCGCCTGCGGATCAGCCAG                         ATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTT
genomic: TTCATCATTTTTATCACTACCCTGAGAGCACTCGCCTGCGGATCAGCCAGgtatgccttc ... cttttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTT




















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: 11 (upstream exon), 73 (downstream exon)
Score: 2

AGCACAGGCGTCATCCAGCTCTAACTTTCTAGTGCTAGGGTTTGCAGCTGTTCATCATTTTTATCACTACCCTGAGAGCACTCGCCTGCGGATCAGCCAGgtatgccttc ... cttttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTTGAGACGATCAATTCTATTTCTGAGTCTGAGAACATATACGATGTGACCA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattattcaaatgtttgattgctctgcttacatgatcttctttgccttttatcagATACTGGTCTTGCCACCTTATCAAGGTGAAGGCCATGGACTTCGTCTTCTTGAGACGATCAATTCTATTTCTGAGTCTGAGAACATATACGATGTGACCA
                        tgcttac  putative branch site (score: 2)
                                   tcttctttgcctttta  putative PPT
        aaatgttt  TA-rich tract