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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag

Basic information

species Zea mays
transcript GRMZM2G019267_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 5'ss of exon 5
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtctt-----gttctag
||||||||||||||| |||||||| |||||||| ||||| |||||||| || |||||||| ||| |||| || ||||||||||||||||| |||||||||||| | | | |    |   ||   || | |  || |||||||  ||  |||| |   |||   | ||||||| ||||| ||| ||||     || | ||
GTACAAGGGGAGCATCTACATGGTCTTCGAGTACATGGATCATGATCTTACTGGGCTTGCAGATAGGCCTGGGATGCGGTTCACTGTGCCTCAGATTAAGgtagaaccacctgtttgtgtgacttgttcttgtttggatgtgatata-ttttgtta-tgacagactgatcttctgatgtgtgatcttctatcgtcccag

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S3_535V6.2 (Physcomitrella patens), 5'ss of exon 3
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag--------------------------------------------------------------
|| ||| ||    ||||||||||| |||||||| |||||||||||||| || || ||||| ||||| || |||||||| ||| || | || || || |||||||  |      |  |  |||  |   || ||   ||||| |     |||| | | |  |    |  ||  |   |   |     ||||||                                                                
GTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCTTGCAGATCGACCTGGAATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtgtagatgaattgc--ttacttcctggtgatgtatttctcttttcttcatttttccttcttcccgctctctctctctctgttctgtcttttgccttatcatttttttcgactcaatcttgaggtttaatatggtcttctataatgcag

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S235_102V6.1 (Physcomitrella patens), 5'ss of exon 4
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacc-tatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag----------------------------
|| ||| ||    ||||||||||| || ||||| |||||||||||| | || || |||||||||||||| || ||||| ||| || | || || || |||||||  | |        |||| || |||||     |   |      || ||   ||| |  |    ||  || ||  |||   | |  |||| |                             
GTTCAAAGGCTCTATTTACATGGTGTTTGAGTACATGGACCATGATTTGACTGGCCTTGCTGATCGGCCTGGGATGCGCTTCTCTATTCCCCAAATCAAGgtacttcgtgggatcaaaccttcactgcttgagcgaattttctctctgtttccttccttacttttctgtcctcgttttgcacagcccagttccaagttttaacatggatcttcttcactgcag

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 5'ss of exon 4
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacct-gcagtgctttgcttag--gatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag--------------------------------------------
|| ||| |||   ||||||||||| |||||||| |||||||||||| | || || ||  | ||||| || || ||||| ||| || | || |||||||||||| |  |    |   | ||  | |||   ||  |    ||| |    ||  |||  |     |  | ||  | |        |  ||||||                                                 
GTTCAAAGGGTCGATTTACATGGTGTTCGAGTACATGGACCATGATTTGACTGGCCTCTCAGATCGACCTGGCATGCGTTTCTCTATTCCCCAGATTAAGgtatattttgaaagagatctcacggtgacctggctgctcgattttatttgacttttacataattttagtggacctccacatgttcttcttgtctcttcattttgtatgggacagtcttaatttgtctcttctacactgtag

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|29130258|gb|CB380962.1|CB380962
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148931632|gb|EC874770.2|EC874770
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|71774594|gb|DR972472.1|DR972472
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|76914973|gb|DV165773.1|DV165773
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148962681|gb|EE013583.2|EE013583
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148946782|gb|EC892051.2|EC892051
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAAGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: C-GGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|148938174|gb|EC882457.2|EC882457
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|211438454|gb|FL012016.1|FL012016
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
EST: gi|211438446|gb|FL012008.1|FL012008
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAG
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAG
EST: gi|211435854|gb|FL011998.1|FL011998
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGAWTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATG
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATG
EST: gi|148942610|gb|EC887630.2|EC887630
EST:     CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAG                         TGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA
genomic: CCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctat ... cttgttctagTGTTACATGAGGCAGCTGCTTACAGGCCTGCACTATTGTCATGTCAACCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGTGCCGCAGATTAAGgtacacctatccaagtacctgcagtgctttgcttaggatgtgtcatggttttatccctgatgaaatgatcttgtgatgcgtggtcttgttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT