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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcctctgatcccgtagcacgagctgtttcagcccgacgagctgggcggtgatgcttgtccgtgtttgatctgtgtggatttagtgcgtagcttc...

Basic information

species Oryza sativa
transcript LOC_Os05g38520.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38520.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G850966_T01 (Zea mays), 5'ss of exon 2
GGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagc--gcctctgatcccgtagcacgagctgtttcagcccgacgagctgggc-ggtgatgcttgtccgtgtttgatctgtgtggatttagtgcgtagcttc
||||||| ||||||| ||||| || || ||||| |||||||||||||| || ||||||||||||||||||||||| || ||||||| | |||||||||||||||||   |||     |   |           |||        || |  |    |||| ||    |  ||||| ||| |    || |||||   | ||    
GGCGCCGCCGCAGCCAAAGTCGGGCCTTTTCGTTGGCATCAACAAGGGTCATGTCGTCACCAAGCGCGAGCTGCCTCCCCGCCCGTGCCACCGCAAGGGGgtaagccaaccttcagccttttgctggtcatcattttgatatcgcgggtggtattggtggtgtgattaagtgttagatgttgtggggtttaggatgcaga---

upper sequence: LOC_Os05g38520.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G009936_T01 (Zea mays), 5'ss of exon 2
GGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagc-gcctctgatcccgtagcacgagctgtttcagcccgacgagctgggcggtgatgcttgtccgtgtttgatctgtgtggatt-tagtgcgtagcttc--
||||||| ||||||||||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||| |  ||||||||| |||||||||||||||||   || | | |   |     | |   |  ||    || |    |   | |  | | |||  |  || | | | |    ||| | | |   ||  |   
GGCGCCGCCGCAGCCGAAGTCGGGCCTCTTCGTGGGCATCAACAAGGGCCATGTCGTCACCAAGCGCGAGCTGCCTCTGCGCCCGTCCCACCGCAAGGGGgtaagccaactttcagcttttttttagggtcat--catgttgatgtcgcgtctgttagtacctgtt-ggattaggtgt-tacatattgtggggttcaggatgct
















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|55432235|gb|CV729137.1|CV729137
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCATTGTG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|55410230|gb|CV722606.1|CV722606
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|163929118|gb|EG710975.1|EG710975
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|11610314|gb|AU165990.1|AU165990
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|286784|gb|D15591.1|D15591
EST:     ACGTCGTCACCAAGCGCGA-CTGCCGCCTCGCCCGTCCGACCGCAAGGGN                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|88434599|gb|CI690875.1|CI690875
EST:     ACGTNGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|88305586|gb|CI631953.1|CI631953
EST:     ACGTNGTCACCAAGCGCGAGCTGCCGNCTCGCCCGTCCGACCGCAAGGGG                         AAAT-CACCAAGAGGGTGANCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|163925615|gb|EG710780.1|EG710780
EST:     CCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: CCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|88422114|gb|CI688909.1|CI688909
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|88719521|gb|CI743031.1|CI743031
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|33654987|gb|CF277601.1|CF277601
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|88728828|gb|CI752338.1|CI752338
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|163925733|gb|EG714569.1|EG714569
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|88724915|gb|CI748174.1|CI748174
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|3760010|gb|C97268.1|C97268
EST:     ACGTCGTCACCAAGCGCGA-CTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|11442728|gb|BF430631.1|BF430631
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|88730456|gb|CI754069.1|CI754069
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGNAAGGGG                         AAATCCANCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
EST: gi|38481097|gb|CF965186.1|CF965186
EST:     ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGG                         AAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT
genomic: ACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcct ... taatttgcagAAATCCACCAAGAGGGTGACCTTTGTCAGGAACTTGATCAGGGAGGTTGCT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGCCGTCGCAGCCGAAGTCCGGGCTCTTCGTGGGCATCAACAAGGGCCACGTCGTCACCAAGCGCGAGCTGCCGCCTCGCCCGTCCGACCGCAAGGGGgtaagcgcctctgatcccgtagcacgagctgtttcagcccgacgagctgggcggtgatgcttgtccgtgtttgatctgtgtggatttagtgcgtagcttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC