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

gtagcctacattttgcactaacactatggcactacatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC

Basic information

species Oryza sativa
transcript LOC_Os01g62810.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G302245_T01 (Zea mays), 3'ss of exon 3
gtagcctacattttgcactaacactatggcactacatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
|||  || |||||  || ||  ||  || || |   ||  |||   || |||  ||| |||| |||||    ||||||  ||||| |||||||||||||| || |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||||| |||||||| ||||| |||||| | ||      
gtaatctgcatttgtcattatgacactgacatt---ttccctg---tatggatatttactgactaaaat---atgtttcttcgaa-gcttcagATTTAGGTCAGGTATGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTCTGGGCTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT

upper sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
gtagcctacattttgcactaacactatggcact-acatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
||| ||| |||       |  || |||| |||| ||||||||     || |||  ||| |||| |||||   | | ||| |||  || ||||||||||||| || || ||||||||||| |||||||||||||||||||||||  |||||||||||||||| |||||||| ||||| |||||| | ||      
gtaacctgcat------atgtcattatgacactgacatttgcccta-taaggatatttactgactaaaat--attttttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT

upper sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G41810.1 (Glycine max), 3'ss of exon 5
----------------------------------------------gtagcctacattttgcactaacactatggcactacatttgctgggctaggg-aactttgctgattaaaactaaatgtt---------ttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
                                               || |    |||||   |  |   | | ||  |   || | ||   ||    |||| ||     ||| ||| |   ||         ||   || || |||||||  ||| |  || |||| ||||||||||||||| |||||||| || || |||||||| ||||| || |  |||||| |||| |||| | | ||      
gtacggaacctttttatggagtatttttacacctaaatctaagattttatctgttattttcttcccattgtgtagcg-tggtttggttgaagtatcacaactatgacttctaagacttaccattgattctggttttctgagagtttcagATACAGGACTGGTGTGGGCTTGGGGCTATGGAGGTGAAGGGCAGCTTGGTCTGGGTTCCAGAATACGTATGGTTTCCACTCCTCATCTTGTTCCTTGCAT

upper sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G40600.1 (Glycine max), 3'ss of exon 7
----------gtagcctacattttgcactaacactatggcactacatttgctgggctagggaactttgctgat-taaaactaaatg---------------ttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC
          || |  |||||| || | |          || |  | |      | || ||||  ||  |||| |||| | | |                 ||||  ||||   ||||||| | || || || |||||||||||||||||||| ||||| || |||||  |||||||| |  |   ||  || || || || |||| ||| | 
gttggctcttgtggt-tacattatgtagttttgtaggttcaatgaagt-atgaagatatggaaggtttttgatgtaaagcaagacacctgatgcatcatatttttaccgaagTTTTCAGATGTGGGACAGGTCTGGGGTTGGGGCTATGGAGGTGAAGGACAGCTAGGATTGGGTTCTCGGGTAAAGATGGTATCATCCCCTCATCTTATAC-

upper sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------gtagcctacattttgcactaacactatg-gcactacatttgctgggctagggaactttgctgat-taaaactaaatgt--tttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
                                                                           ||  ||     ||| |  |  ||| |  |  |||     | |  | || | |  || |  ||  |   | | | |||  |||   | ||| ||||||| |||| || || ||||||||||||||||| || |||||||| || ||  ||||||||||||| || |  || |||||||| ||||   | ||      
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgca--ttcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT

upper sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G03870.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------gtagcctacattttgcactaacactatggc----actacatttgctgggctagggaactttgctgattaaaactaa---atgt------------tttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
                                                        |  | || ||  ||   |||   | |||      |   | ||  || | || ||||  |   | ||  || ||||   ||||            |||   |  || ||||||| |||| || || ||||||||||||||||| || |||||||| || ||  ||||||||||||| || |  || |||||||| ||||   | ||      
gtattgactttattatgaactatttgtcaacctaggtctaaaattttatctgttattttcgtatatgatgtgataatcttttggttgaagcagaactttttgtgttatggaagatcagttatgcaatctaagacatgtcattgattgtaattttctgtgagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT

upper sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G53830.1 (Arabidopsis thaliana), 3'ss of exon 5
----------gtagcctacattttgcactaacactatggcactacatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
           ||  | || |||| ||    |   |||   || | |    ||   | |   | |    |||  |  |    |||||||  || ||| |||||||||||| ||  | ||||||||||| |||||||| ||||| ||||||||  |||||||  | ||    |  || || ||||| ||||  || ||      
gtgaagttgaataaacgactttttacaaatccgagatgaagctgc-taccttgtagttgaagattcatttgaggatgatc--atgtttttacggaagtttcagATTTAGGACAGATTTGGGGTTGGGGATATGGAGGCGAAGGTCAACTAGGATTGGGTTCCCGGATTAAAATGGTGTCATCTCCTCATCTAATACCTTGCCT

upper sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0007g00930.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------------------gtagcctacattttgcactaacactatg-------gcactacatttg-----ctgggctagggaactttgctgat-taaaactaaatgt----tttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
                                                          | |   |    ||||   | |||||||        | |   ||||||     |   |||| ||||  |   | || |||| | | |       |||  | |||| ||||||| | || || || |||||||||||||||||||| |||||||| |||||  |||||||| | |    |   || || ||||| ||||  || ||      
gtaaattctccatcccctgggtcactgcagcccacacaagccacagttttcaggtgtagcaatttcttctttgtggttacactatatagttttgtaggtcatttgaagtacgaagctatggaagatctttaatgtaaagcaagacacctaatttaacaaaagtttcagATATGGGACAGGTGTGGGGTTGGGGCTATGGAGGCGAAGGGCAGCTAGGTTTGGGTTCTCGGACAAAGCTGGTGTCTTCTCCTCATCTCATACCTTGCTT

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|29664300|gb|CB660575.1|CB660575
EST:     TAAAATAATGGCAGTAGCTGCTGGTGGTCGTCATACATTAGCACTATCAG                         CTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAAC
genomic: TAAAATAATGGCAGTAGCTGCTGGTGGTCGTCATACATTAGCACTATCAGgtagcctaca ... ttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatttgctgggctagggaactttgctgattaaaactaaatgttttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC
                                  aactaaa  putative branch site (score: 2)
                                         tgttttctc  CT-rich tract
                             attaaaactaaatgtt  TA-rich tract