Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttccttaccttattatggttcacctggaagaatgtagcttttgcttaattaacaatatttttcaatgctgcaatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g61810.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G840909_T02 (Zea mays), 5'ss of exon 4
CAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttccttaccttat-tatggttcacctggaagaatgta----gcttttgcttaattaacaatatttttcaatgctgcaatgcag
|||||||||||| ||||||||| |||| || |||||||| |||||||| ||||| || |||||||||||||| || ||||| |||||||| ||||||||||||  || |||| ||||  |||  ||||  ||  ||||| ||    || | |   | || | |||| || |||||||||| | |||||
CAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGATTAAGgttgatttcttaacttacatattcttcatatgatagaatatatggagcatgttactgat-agcaatcttgttcaatgctgtactgcag

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA15G20970.2 (Glycine max), 5'ss of exon 4
CAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttag---ttccttaccttattatggttcacctggaagaatgtagcttttgcttaattaacaatatttt--tcaatgctgcaatgcag-------------
  ||||| |     | || ||  | |||||||||||||| ||||| || |||||||||||||| ||||| || || ||  | || || |||||  |||||||| |   |  | |   || |    | |   |        | || |||||  | | || |||| | |||  | || | | ||||   |             
TGAAAAGTTAAACCAGATAGAACTTTCAGACTGTGAAATATATGCTTCTTGTGAACCTTGCCCTATGTGCTTTGGAGCAATTCACCTCTCACGAGTTAAGgttggaaatgtcctgttttttctacgcttctcaatttatctataccttttattaattttacaagaatttaattaaag-tacaattttgtgtacaatagttc

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA16G22830.1 (Glycine max), 5'ss of exon 8
CAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttag---ttccttaccttat-tatggttcacctggaagaatgtagcttttgcttaattaacaatatttt--tcaatgctgcaatgcag-------------
  ||||| |     | || ||  | |||||||||||||| ||||| || |||||||||||||| ||||| || || ||  | || || ||| |  |||||||| |   |  | ||  || | |||| |||  |        | || |||||  | | || |||| | |||  | || | | ||||   |             
TGAAAAGTTAAACCAGATAGAACTTTCAGACTGTGAAATATATGCTTCTTGTGAACCTTGCCCTATGTGCTTTGGAGCAATTCACCTCTCAGGAGTTAAGgttggaaatgtcctattttttatatgcttc-tcaatttatctataccttttattaattttacaagaatttaattaaag-tacaattttgtgtacaatagttc

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G09430.2 (Glycine max), 5'ss of exon 3
CAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttag---ttccttaccttattatggttcacctggaagaatgtagcttttgctta-attaacaatatttttcaatgctgcaatg-cag------------
  |||||||     | || ||  | |||||||||||||| ||||| || |||||||||||||||||||| || || ||  | || || |||||  |||||||| |     || | | || |    | |   |        | || |||||  | |  |||| |  ||||    |   | || |   ||            
TGAAAAGCTAAACCAGATAGAACTTTCAGACTGTGAAATATATGCTTCTTGTGAACCTTGCCCAATGTGCTTTGGAGCAATCCACCTCTCACGAGTTAAGgttggaaacgccctgctttttctacgcttctcaatttatctttatcttttattaatgttaaaagaatttcattaaagtacattaatagtagtgtaaaagt

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA09G09440.1 (Glycine max), 5'ss of exon 4
CAAAAAGCTTG-GAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagt--tccttaccttattatggttcacctggaagaatgtagcttttgcttaattaacaatatttttcaatgctgcaatgcag
      ||||| |||||  | |          |||||| ||||||| || |||||||||||||||||||| || |  ||  | |  || |||||  |||||||| |   | |    ||| |  |      |         | |   || |  | | || ||||  ||||| | |            
------GCTTGTGAAAAGCTAAACAAGATAGATGTGAAGTGTATGCTTCTTGTGAACCTTGCCCAATGTGCTTTgtagcaatccccctctcacgagttaaggttggaaatgcccttcttttcctacccttctcatttttcttttcattatattaattttacaa-gttttttatta-----------

upper sequence: LOC_Os03g61810.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv14s0030g01610.t01 (Vitis vinifera), 5'ss of exon 4
CAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgtt--agttccttacct------------tattatggttcacc-tggaagaatgtagcttttgcttaattaacaatatttttc--aatgctgcaatgcag---
 || |||||     |||||||| | |||||||||||||| ||||| || ||||| |||||||||||||| || || ||| | ||||| ||| | ||||||||   | | || ||| |            |  ||  ||| ||| | | | | |  |||  || | |||| |    |||  |||  | ||||    ||| |   
TAAGAAGCTCAATCAAATTGAGCTATCAGACTGTGAAATCTATGCCTCTTGTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAATTAAGgtctaaataccctacgtctcttcattttcttctaacgttaaccatcgtacattacagcaatttcctaatcatttttatccttcgtattgctcttttgccgcag

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|58691571|gb|CK080258.1|CK080258
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88555582|gb|CI485850.1|CI485850
EST:     TTTCGGCGCTNTGCATCTATCACGGATTAAG                         AGGCTGGTTTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: TTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|86526937|gb|CI167143.1|CI167143
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88530960|gb|CI459394.1|CI459394
EST:     TGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: TGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88842879|gb|CI371779.1|CI371779
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88554790|gb|CI484994.1|CI484994
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|27547275|gb|CA765405.2|CA765405
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|66916794|gb|CX103642.1|CX103642
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88526990|gb|CI455094.1|CI455094
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|89167816|gb|CI021515.1|CI021515
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|58688225|gb|CK076912.1|CK076912
EST:     GTGAACCTTGCCCACTGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AAGCTGGTGTATGGAGCCAAAGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|25806978|gb|CA762939.1|CA762939
EST:     GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: GTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
EST: gi|88466860|gb|CI539656.1|CI539656
EST:     CCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAG                         AGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT
genomic: CCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGAT

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: 60 (upstream exon), 65 (downstream exon)
Score: 19

CAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGATTAAGgttagttcct ... tgcaatgcagAGGCTGGTGTATGGAGCCAAGGCAGAAGCTGCTATTGCCATTGGATTCGATGACTTCATTGCTGATGCTTTGAGGGGAACTGCTTACTACCAGAAGGCCA




<











<


<