Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGCCCTCTGGGGAAAGCTGGCAGCAGAAATCCTAATGCAGAACTGGGACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaacttcaatgttttgttctgtgttctttgttctttgtgtacactatatcaccaaccatgttccttcctgatctttgggcag

Basic information

species Zea mays
transcript GRMZM2G151549_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151549_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G33770.1 (Glycine max), 5'ss of exon 3
GAGTGCCCTCTGGGGAAAGCTGGCAGCAGAAATCCTAATGCAGAACTGGGACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaact-tcaatgttttgttctgtgt------tctttgttctttgtgtacactatatcaccaacc---atgttccttcctgatctttgggcag-----------------------------------
||||||  | ||||| ||||||||||| |||||  | ||||||||||||||| | ||| | || || ||||| |||||||||||||| ||||||||||||||| |   | |   |   ||| ||| ||       |   |||||||  |   || |  |||          |||    ||| || |  ||  ||                                     
GAGTGCATTGTGGGGGAAGCTGGCAGCTGAAATTTTGATGCAGAACTGGGACATTGCTCTTGAAGAGCTCAATCGCTTGAAGGAAATCATTGATTCAAAGgttgttcttgtttgtcagttgatctttggagtagatgcatgttcttgtttgtcagttgatctttggagtagatgcatgttcttgtttgttatgcttaatatattaatatagactggtgaacttcgttgcag

upper sequence: GRMZM2G151549_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G16090.1 (Glycine max), 5'ss of exon 3
GAGTGCCCTCTGGGGAAAGCTGGCAGCAGAAATCCTAATGCAGAACTGGGACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaact-tcaatgttttgttct---------gtgttctttgttctttgt-gtacactatatcaccaaccatgttccttcctgatctttgg-gcag
||||||  | ||||| ||||||||||| |||||  | ||||||||||||||| | ||| | || || |||||||||||||||||||| ||||| ||||||||| |   | |   |   ||| |||          ||    || || ||||| || |   | ||    ||    |     |  ||| |||||  ||||
GAGTGCATTGTGGGGGAAGCTGGCAGCTGAAATTTTGATGCAGAACTGGGACATCGCTCTTGAAGAGCTCAACCGCTTGAAGGAAATCATTGACTCAAAGgttgttcttgtttgtcagttggtctttggagtagatgcatgttcttgtttgttgtgcttaaaatatttaatatagactggtggtgaactttgttgcag
















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|148947189|gb|EC892527.2|EC892527
EST:     ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaactt ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|149086591|gb|EE176135.2|EE176135
EST:     ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaactt ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|148945927|gb|EC891220.2|EC891220
EST:     ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaactt ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|71772604|gb|DR970532.1|DR970532
EST:     ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaactt ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|211543296|gb|FL204964.1|FL204964
EST:     CGTAGCTTTGGAGGAAACTCA-CCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: CGTAGCTTTGGAGGAA-CTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaactt ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|148932020|gb|EC875324.2|EC875324
EST:     ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaactt ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
EST: gi|148942799|gb|EC887829.2|EC887829
EST:     ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAG                         AACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT
genomic: ACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaactt ... ctttgggcagAACTTCTCATCACCTCTGAATCAGCTCCAGAACAGGATATGGCTGATGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGCCCTCTGGGGAAAGCTGGCAGCAGAAATCCTAATGCAGAACTGGGACGTAGCTTTGGAGGAACTCAACCGCTTGAAGGAAATAATTGATTCAAAGgttctaacttcaatgttttgttctgtgttctttgttctttgtgtacactatatcaccaaccatgttccttcctgatctttgggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA