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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTCCCAAAGAGCTGATGGGTTGTTGCAAAGCTTAAGATTGCGATACCCTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAGgttattcctcacattttatcttagttgaatatgtcaaacaagttgggcacttgggcttagagttagcattgtatggttcattcaccttctatttcatcaa...

Basic information

species Oryza sativa
transcript LOC_Os09g37270.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g37270.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G105253_T03 (Zea mays), 5'ss of exon 3
TTTGTCCCAAAGAGCTGATGGGTTGTTGCAAAGCTTAAGATTGCGATACCCTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAGgttattcctc-------acattttatc-ttagttgaatatgtcaaacaagttgggcacttgggcttagagttagcattgtatggttcatt---caccttctatttcatcaa-----------
||||||  |||||||| ||||  | ||||| ||| |||||||| |||| |||||| ||||||||||||| || ||||||||||||||||||||||||||||| |  |||        |||  | | |      | | | || | || |        |    | |||    ||   |||  |    ||||      |  | | |||| |  |           
TTTGTCTGAAAGAGCTAATGGTCTATTGCAGAGCCTAAGATTGAGATATCCTGGTCTGCCACAAACCTCCCTTGACATGAACAAGATCCAGTATAACAAGgtaaagcctgtgcaaagacaagtaaccacctacttattctggccaaaacacaattgataaagtctttttctttcaattacacaaatcataatattcactttgtttctttgaaaatttcccag

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G158679_T01 (Zea mays), 5'ss of exon 4
TTTGTCCCAAAGAGCTGATGGGTTGTTGCAAAGCTTAAGATTGCGATACCCTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAGgt--------------------tattcctcacattttatcttagttgaat--atgtcaaacaagttgggcacttgggcttagagttagcattgtatggttcattcaccttctatttcatcaa
||||||  |||||||||||||  | ||||| |||||||||||| |||| || ||  |||||||||| || || |||||||||||||| ||||||||||||||                    ||  | |    || |    | |   |||  |  || | |||||    |  |  |    | |     || | |    ||  ||   |||   | |  | | 
TTTGTCTGAAAGAGCTGATGGTCTATTGCAGAGCTTAAGATTGAGATATCCAGGCCTGCCACAAACTTCCCTTGACATGAACAAGATACAGTATAACAAGgtaaagctcatgcaaaaacaaataaccatggacttcttctctggccaaatcaaaatcgatcaagtctttctttcagttacacaaaccacaatcttcactttgtt--tcttgcgtgtttttag

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S283_2V6.1 (Physcomitrella patens), 5'ss of exon 6
-TTTGTCCCAAAGAGCTGATGGGTTGTTGCAAAGCTTAAGATTGCGATACCCTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAGgttattcctcacattttatcttagttgaatatgtcaaacaagttgggcacttgggcttagagttagcattgtatggttcattcaccttctatttcatcaa-
  ||| |  | | ||| ||     ||||||| | ||| |  ||||| | ||| || || ||||||||  | || ||||||||||||||||||||||||||||| || |    |  | |||| | |||   ||       ||| |   |    ||    | |      || |||    || |   |   |    || |  |  
GATTG-CTGATAAAGCAGAGACTATGTTGCACACCTTGAAGTTGCGGTTCCCAGGGTTACCACAAACTGCCCTTGACATGAACAAGATCCAGTATAACAAGgt-atgcacacctgtatatcattgtttcttaaaggttgcaattgttgttgatgcatattggcgccccaatgttaaatttaactagaattcgcttgactata

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S22_225V6.1 (Physcomitrella patens), 5'ss of exon 6
-TTTGTCCCAAAGAGCTGATGGGTTGTTGCAAAGCTTAAGATTGCGATACCCTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAGgttat----tcctcacattttatcttagttgaatatgtcaaacaagttgggcacttggg-cttagagttagcattgtatggttcattcaccttctatt-tcatcaa--------------------------------------------------------------------------------------
  ||| |  | | ||| ||     ||||||| ||||| |  || || | ||| || |||||||||||| | || || ||||||||||| ||||||||||||||  |    ||| |   |    | || |||   | ||||| |   |  |   | |||   |  |  |||| | || |    |     |    |  | | | ||| |                                                                                      
GATTG-CTGATAAAGCGGAGTCTATGTTGCATAGCTTGAAGTTACGGTTCCCAGGGTTGCCACAAACCGCCCTTGATATGAACAAGATTCAGTATAACAAGgtagtcgcatccccgtgtcaattttttgtttgct-tgtcatagttgacgtttatttgcatcccaatgttatccttttggaatctgcccgtgatgaactgtaatctacatcatgtgaggctgtagtcgtctctgcaattcatttttatgtcgttgctattggagctgactgggttttcgtcttctgcacgtag

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|86496451|gb|CI139084.1|CI139084
EST:     AACAAGATCCAGTATAACAAG                         GACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTG
genomic: AACAAGATCCAGTATAACAAGgttattcctc ... tcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTG
EST: gi|33802569|gb|CF327157.1|CF327157
EST:     CTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAG                         GACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTG
genomic: CTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAGgttattcctc ... tcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTG