Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaccaagaacatgcaatcactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC

Basic information

species Oryza sativa
transcript LOC_Os01g70190.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
gtgagcaccaagaacatgcaatcactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatga---acctgctttatgc----aatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
         | |    | |  ||| |  | |  |||| ||||  |   |||||||   |||| || | || |||| |||||    |||| |  ||| |    ||||||| || ||||||||||| || |||||||||||||||||||| || || || |||||||| || ||||||||||| || ||||||||||||||||||||| ||
-------gtacgtcgctaccttcattgcacg--tcctaataacaagccttgatgagccattg-aatcaaagagtcctgatgtgctacctaccgtatacttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC

upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
gtgagcaccaagaaca-tgcaatcactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatgaacctgcttt-atgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
    |||  |||     | | ||  || ||||||| |  |  |  |    | |  ||| | ||   |  |||  ||    |||   | ||||  |    | |||||||||| | ||| | |||||||||||||| ||| ||||||| || |||||||| |||||||| || ||| |||| ||||||||||||||||| ||  | 
---tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataac-aataaatgatcctgaaagctcaaactgactgtacttttgtatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT

upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 3
gtgagcaccaagaacatgcaatcactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttga--tgaacctgcttta-tgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
 | ||||   |  |  |    |   || |||  |    |||  ||      ||||   |   | | ||  ||  ||  |  |||   | ||||  |    |  ||||||||| | ||| | |||||||||||||| ||| ||||||| || |||||||| ||||| || || ||| |||| || |||||||| ||||| ||  | 
-taagcatgcatgaagtttggt---tccatgtcttgatatac-caaaacaaatgacaaaaaatgatcctgaaagctcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA

upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
gtgagcaccaagaacatgcaatcactcgatgcttcctcat--aagcattgttg-atgaattattgtaacccaaaagtcttgatgaacctgctttatg-caatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
 |||       |  ||||||||     ||||||| |  |   || ||   ||| || ||  | |    |       |     ||| | || |||       |||||||| ||  | ||| | |||||||||||||| ||| ||||||  || |||||||||||||| || || ||| | || |||||||||||||||||  |  ||
atgaa-gtttggtgcatgcaat-----gatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC

upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G27440.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagcaccaagaacatgcaatcactcgat--gcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
   |  |  ||| |      || |     |  | ||    |||||  | | | |      |||||     ||    ||   || | || || | |    |  ||||||||  | ||| ||||||||||||||||||||||||| ||| | ||||||||||| ||||| |||||  |||| |||||||| ||||||||| |  ||
---acaattaagcattcctcattaggaagttaggttatatataaggttagctaagatcaaattgttttagaatctgctgactggaacttctctct-ttgtatagAGGTGCAAGAGCAGCGGTGTGGGAGAACTTCAAGAACAACCCTTTGTTTGACATCTCAACAGATCACCCGACAACATACTACGAAGACATGCAGAGAGCC

upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------------------------------------------------------------------gtgagcaccaagaacatgcaa-tcactcgatgcttcctcataagcattgttgatgaattattg--taacccaaaagtct-tgatgaacctgctttatgcaat----gcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
                                                                                       |  | |    | ||||  || |||    | |     | || ||  |  ||   ||   || |  |   |  | | ||  ||||||   |  ||| |  ||      ||| |||||  | ||| | || ||||| ||||||||  ||||||| || ||||||||||| ||||| |||||| |||| || || |||||||||||| |  | 
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA

upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
gtgagcaccaagaacatgcaatcactcgatgcttcctcataagcattgt---tgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
    |      |  | |  | |    | ||| |   | ||| | | | |     | ||  | || ||| ||||   | ||  |       | || |    |||||||| || || ||| | ||||||||||| || ||  ||||||| |||||||||||||| ||||| ||||||   || || || ||||||||||| ||  | 
-attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttt----tgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT

upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ05285 (Selaginella moellendorffii), 3'ss of exon 3
gtgagcaccaagaacatgcaat-cactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
                |  | | | ||| || | |    | |||| |||||    ||  ||  ||  ||    ||  |||      |  | |   || ||||| ||||| |||||  | || |||||||| |||||| | |||||||| ||||||||||| || || |||||    || ||||| ||||||||||||||  | 
---------------gtaaagttctctcaatacata--gaaaagctttgtttgaaaag-atcttattcc----gttctgaca----ttttctgctca-tgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTATGAGGACATGCAGCGAGCT

upper sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
gtgagcaccaagaacatgcaat-cactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
                |  | | | ||| || | |    | |||| |||||  ||||    | | |  |    ||  |||   |  ||||       |||||| ||||| |||||  | || |||||||| |||||| | |||||||| ||||||||||| || || |||||    || ||||||||||||||||||||  | 
---------------gtaaagttctctcaatacata--gaaaagctttgtt--tgaaaagatcttattc---ggttctgac--atttgctgc---tcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT

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|88737382|gb|CI760890.1|CI760890
EST:     GGTTTATTCTATGATACCGCAAATGATCCTGAGGGTGGTTACTATGCAAG                         AGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGA
genomic: GGTTTATTCTATGATACCGCAAATGATCCTGAGGGTGGTTACTATGCAAGgtgagcacca ... tgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGA
EST: gi|29671328|gb|CB667603.1|CB667603
EST:     GGTTTATTCTATGATACCGCAAATGATCCTGAGGGTGGTTACTATGCAAG                         AGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGA
genomic: GGTTTATTCTATGATACCGCAAATGATCCTGAGGGTGGTTACTATGCAAGgtgagcacca ... tgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGA

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: 69 (upstream exon), 72 (downstream exon)
Score: 11

CTCACCTTGTTCCCCCAGAGACACCTCGATCAATCTTTGTCTATTTCCGTGGTTTATTCTATGATACCGCAAATGATCCTGAGGGTGGTTACTATGCAAGgtgagcacca ... tgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
       aattattgtaa  TA-rich tract