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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG

Basic information

species Oryza sativa
transcript LOC_Os02g54340.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 4
gtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
|||| |||||||  |   |||||  | |   |||  |    |        ||| |||  | |  |||   || |  | |  || ||| | |||||||| ||||| || ||||||||||| |||||||||||||| |||||||||||||| || ||
gtatgccatgctcgtgtcatttttctcatctcatgccaccta-------gaatttgtgcagcttttt---atgccttgtaatgaatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 4
---gtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcatt-----cagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
    | |   |||||     || |    |||        |  |  ||||        |||||  ||   | |   | |   || ||  |   |     |||||||| ||||| ||||| || || ||||| || |||||||| |||||||||||| | || ||
gtcttgtcttatgctatgtgaaatgccatgattttcccccccttttgaagttgc-catgttgcacctaatataccattaccttctgctttgatgatggcagTTTGTTGTTGGGCTAGGAGACAAGGTTTCCCCCACTGACATAGAGGAAGGGATGCGTGTTGG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------------------------gtattccatgcttatccaattttattga--aacca--tatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcatt--cagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
                                                                        | |   || |||    || | | |     | ||  | ||||   |     ||||||    | |   | |   ||||  | |  | |    ||   ||||||| ||||| ||||| || || ||||| || ||||||||||||||||||||| | || ||
gtacctataatttttttaacaatcttttcatctttcccttttctagttgtttgtttgaagatgtttggcttcacttgttgattaagagatatcacttgctgatcagttgtcttatgttttgtaaaatgccaagttgggtctaatataccttctgctttgatgttgatagTTTGTTGTTGGGCTAGGAGACAAGGTTTCCCCCACTGACATTGAGGAAGGGATGCGTGTTGG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------gtattcc-atgcttatccaattttattgaaaccatatctttcatgaa--aaaaaatgtgttgatccctttctc-atactgta--------------ttttgtatcatt-------cagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
                                                                              || |    ||| |   |     ||| ||  |  | ||  |  |||       |||  ||||||| | |||||  || ||||               || ||  |  ||       |||||||| ||||| || || ||||||||||| || || |||||||||||||||||| | || ||
gtaatctatattttcaacaatgtgaagaagatgccaaactgtcccattgtttctcaccacatttatcctatattcttggtttgaagatgttagacttcacttactgttatgaaattgtcaatgggttggcaaagctgttgattcttttctttatgctgtcaggactaataatccttctgcgttctttttatgacagTTTGTCGTTGGGCTGGGTGATAAAGTTTCACCTACCGACATTGAGGAAGGGATGCGTGTTGG

upper sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------gtattcca--tgcttatccaattttattgaaaccatatctttcatgaa--aaaaaatgtgttgatccctttctcatactgta--------------ttttgtatcatt-------cagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
                                                                          || ||  |  || |   |     ||| ||  |  | ||  |  |||       |||  ||||||| | ||  | || ||||               || ||  |  ||       |||||||| ||||| || || || |||||||| || || |||||||||||||||||| | || ||
gtaatctatattttcaacaatgtgaagatgccaaactgtcccattgtttttcaccacatctatcccgtgttcttgttttgaagatgttagacttcacttactgttatgaaattatcaatgggttggcaaagctgttgattctttgattatgctgtcaggactagtaatccttctgcttttttttaatgacagTTTGTCGTTGGGCTGGGCGACAAAGTTTCACCCACCGACATTGAGGAAGGGATGCGTGTTGG

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|58603359|gb|CK013887.1|CK013887
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|29684844|gb|CB681119.1|CB681119
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58685776|gb|CK074463.1|CK074463
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58602175|gb|CK012703.1|CK012703
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATCAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|58675342|gb|CK064029.1|CK064029
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGG
EST: gi|88574346|gb|CI666115.1|CI666115
EST:     CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAG                         TTTGTGGTTGGCCTAGGGGATAAAGTTTCCTCCA-CTGACATTGAGGAA
genomic: CTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatg ... tatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTC-TCCAACTGACATTGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcagTTTGTGGTTGGCCTAGGGGATAAAGTTTCTCCAACTGACATTGAGGAAGGGATGAGAGTGGG
                tgttgat  putative branch site (score: 4)
      aaaaaaaatgtgtt  TA-rich tract