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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatagtgcctatgtttacctatagagtgccgttatggtggtctctattgttagtattctactaccagcattgttgtcgatatgcttttaaatgcagaaatgtgaaatacaatacactgatcattatgcatttttgttatttagCTTACGGCCTACCATGAAAGTGGGCATGCTATTGTTGCACTCAACACCCAGGGTGCCCACCCCATTCACAAGGCTACTATCCTGCCTCGTGGCTCTGCCC

Basic information

species Oryza sativa
transcript LOC_Os01g43150.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 13
gttatagtgcctatgtttacctatagagtgccgttatggtggtctctattgttagtattc-tactaccagcatt--gttgtcgatatgcttttaaatgcagaaatgtgaaatacaatacactgatcattatgcatttttgttatttagCTTACGGCCTACCATGAAAGTGGGCATGCTATTGTTGCACTCAACACCCAGGGTGCCCACCCCATTCACAAGGCTACTATCCTGCCTCGTGGCTCTGCCC
      |    | |||||   | ||   | || || |||        |     ||      || | | | |||   |||| | ||    | |  | || || |   ||       ||    | |   | ||   ||| ||||  ||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||| |||||||| |||||||| |||||||| |||||||
------gcatgtttgtttttgt-taacttacctttttggcaagtaaaaagaaaagagcgagtagtcctaacataaggttgcc-atgaagtctagattggagcagc-tgtgcggatatgtgattaatttcatttctttgtgttcattagCTTACTGCCTACCATGAAAGTGGACATGCTATTGTTGCACTCAACACCCAGGGTGCTCACCCCATACACAAGGCAACTATCCTTCCTCGTGGGTCTGCCC

upper sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 13
gttatagtgcctatgtttacctatagagtgccgttatggtggtctctattgttagtattctactaccagcatt-gttgtcgatatgcttttaaatgcagaaa-tgtgaaatacaatac-actgatcattatgcatttttgttatttagCTTACGGCCTACCATGAAAGTGGGCATGCTATTGTTGCACTCAACACCCAGGGTGCCCACCCCATTCACAAGGCTACTATCCTGCCTCGTGGCTCTGCCC
        || | | | |   | |  | |  | || |  | |   |||     |  | | || | | | |||  | | || |||   | |  | || || || || |||||   |||  | | | | | ||    || || |  ||||||||| || |||||||||||||| |||||||||||||| ||||||||||||||||| |||||||| ||||| || |||||||| |||||||| |||||||
--------gcatgtttgtttttgttaactttcctttt--tcgcaactaaaaagaacaat-tagtcctaacataaggtttccataaattctagattggagcaactgcgaaatcgtatattaattaacttcatttccttgtgctcattagCTTACTGCGTACCATGAAAGTGGACATGCTATTGTTGCGCTCAACACCCAGGGTGCTCACCCCATACACAAAGCAACTATCCTTCCTCGTGGGTCTGCCC

upper sequence: LOC_Os01g43150.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 13
gttatagtgcctatgtttacctatagagtgccgttatggtggtctctattgttagtattctactaccagcattgttgtcgatatgcttttaaatgcagaaatgtgaaatacaatacactgatcattatgcatttttgttatttagCTTACGGCCTACCATGAAAGTGGGCATGCTATTGTTGCACTCAACACCCAGGGTGCCCACCCCATTCACAAGGCTACTATCCTGCCTCGTGGCTCTGCCC
                                 || |  |  | |||  ||||   | | || ||  |   ||  | |  |  |  || |  ||| | |  | || | |  ||||      |  || || |  |||       ||||||| || || ||||| ||||| ||||| ||||||||  | |||||  ||||||| || || ||||||||||| || ||| |||||||||| |||||  
-------------------------------aatttttataatttct--tgtttagagt-taataaaatatttagtatttaactatttattgatgtacagttatgtattttaatat-----tgcttgtgaaacttt------cagCTTACTGCTTATCATGAGAGTGGCCATGCAATTGTTGCTATTAACACTGAGGGTGCTCAACCAATTCACAAGGCAACAATCATGCCTCGTGGATCTGCTT

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: 58 (upstream exon), 75 (downstream exon)
Score: 27

TATTATCATGGGAACTGAGAGGAAATCAATGTTCATATCTGACGAATCCAAAAAGGCATGCCTCTTCAAGTTACTTTATTTTATTTTAAGAGAGTTAATAgttatagtgc ... tgttatttagCTTACGGCCTACCATGAAAGTGGGCATGCTATTGTTGCACTCAACACCCAGGGTGCCCACCCCATTCACAAGGCTACTATCCTGCCTCGTGGCTCTGCCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgcagaaatgtgaaatacaatacactgatcattatgcatttttgttatttagCTTACGGCCTACCATGAAAGTGGGCATGCTATTGTTGCACTCAACACCCAGGGTGCCCACCCCATTCACAAGGCTACTATCCTGCCTCGTGGCTCTGCCC
                         cactgat  putative branch site (score: 27)
                                         tttttgtt  putative PPT
                                 attatgcatttttgtt  TA-rich tract