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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCACATGGATTTACATCTGCTTCCCCTTCCATTATTGAAGAAAGCATTCCTGTTGTTGACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaatttcttcctcagctcttttacattcttaatttggttgtttctcttatccataatctcgttcaaagttgaaattaatactcaaatcgttgtt...

Basic information

species Oryza sativa
transcript LOC_Os05g46720.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46720.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G174990_T03 (Zea mays), 5'ss of exon 12
GCAGCACATGGATTTACATCTGCTTCCCCTTCCATTATTGAAGAAAGCATTCCTGTTGTTGACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaatttcttcctcagctcttttacattcttaatttggttgtttctcttatccataatctc--gttcaaagtt--gaaattaatactcaaatcgtt--gtt----------------
                  | || | | | | |   ||||||||||| |||||||||||| |||||||||||||||||||||||||| | ||| |||| |||| |   |    |||| |||| | || |   || ||| | || ||| |||| ||||    ||||||  |   ||||||  |   || ||  |  |  ||||  |||                
------------------TTTGTTGCTCATGCTTCTATTGAAGAAAACATTCCTGTTGTAGACAAGGTTGTGGATGATGGATGGGGTACTCCCAGAGGTAGTCTCCAAG---CTTCTTCAGgtattctgtgttatta-tatgattgcttcttttattgtgaatctcttgcctaaagttttgttcttcattttacatccgttcagtttattttagtcgatgtc

upper sequence: LOC_Os05g46720.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G355610_T01 (Zea mays), 5'ss of exon 12
GCAGCACATGGATTTACATCTGCTTCCCCTTCCATTATTGAAGAAAGCATTCCTGTTGTTGACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaatttcttcctcagctcttttacattcttaatttggttgtttctcttatccataatctc--gttcaaagttgaaattaatactcaaatcgttgtt--------------------
                     | |   | | |   ||||| ||||| |||||||||||| |||||| |||| |||||||||||||| ||||| ||| |||||     |  | |||| |||| | || ||  ||  || | |  |||||| | ||||    ||||||  |   ||||||    ||  |  |   |     | |                    
---------------------GTTGTTCATGCTTCTATTGGAGAAAACATTCCTGTTGTGGACAAGATTGTTGATGATGGATGGGGTAGTCCCAGATCTAGTCCACAAGCTGCTTCTTCAGgtattctatgttggta-tataattgtttattttattgtgaatctcttgcctaaagtttttgttcttcattttacatccgctcagttttagttagcccatgt
















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|29624626|gb|CB629637.1|CB629637
EST:     GTGGATGATGGATGGGGCAGTCCTAGAGCTA                         GTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
genomic: GTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaat ... ttcacgccagGTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
EST: gi|25798655|gb|CA754616.1|CA754616
EST:     TTGTTGACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTA                         GTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
genomic: TTGTTGACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaat ... ttcacgccagGTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
EST: gi|11025950|gb|AU162551.1|AU162551
EST:     GACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTA                         GTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
genomic: GACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaat ... ttcacgccagGTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
EST: gi|4881160|gb|AU065459.1|AU065459
EST:     GACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTA                         GTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
genomic: GACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaat ... ttcacgccagGTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
EST: gi|29665230|gb|CB661505.1|CB661505
EST:     ACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTA                         GTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
genomic: ACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaat ... ttcacgccagGTTCATCACCCTCGAGAAGTTTGCCTATCACATTTGATGGCCTCTGGACAC
EST: gi|29628535|gb|CB633546.1|CB633546
EST:     TCCTGTTGTTGACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGATA                         GTTCATCACCCTCGA
genomic: TCCTGTTGTTGACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaat ... ttcacgccagGTTCATCACCCTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCACATGGATTTACATCTGCTTCCCCTTCCATTATTGAAGAAAGCATTCCTGTTGTTGACAAGGTTGTGGATGATGGATGGGGCAGTCCTAGAGCTAgtatggcaatttcttcctcagctcttttacattcttaatttggttgtttctcttatccataatctcgttcaaagttgaaattaatactcaaatcgttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctc