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

CAGCAATCTGTGGCTCTTGGCAATACGGCAAATCCAAGGGCTAGGTACTGTAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatatggatcagctttatgttttgccagctgtcatgaatcgactaatatcatttttgtgtgctttgcctctacatgatttcag

Basic information

species Zea mays
transcript GRMZM2G027307_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027307_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g58960.1 (Oryza sativa), 5'ss of exon 2
CAGCAATCTGTGGCTCTTGGCAATACGGCAAATCCAAGGGCTAGGTACTGTAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagt-------atat------ggatcagctttatgttttgccagctgtcatgaatcgactaat-atcatttttgtgtgctttgcctcta--catgatttcag
|| |||||| | ||||      | || | | |||||||||||||||| |||||||| ||||||||| ||||||||||||| ||||| |||||||||||||||||||        |||      ||||||  ||| |||| | | || | | |||||| |  || | | || | ||||||  |||  | |||  |||| ||||||
CAACAATCTATCGCTCACAATGACACAGGACATCCAAGGGCTAGGTATTGTAGGAAGTGCAACCAGATGAAGCCACCTCGATGCCATCATTGCTCTGTTTgtaagttgttgatttattcttcaggatcaattttttgttgttctagttattatgaattgtatagtcaacaatattgtgta-tttatcactaatcatggtttcag
















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|5895854|gb|AW037100.1|AW037100
EST:     CGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: CGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|148930766|gb|EC873088.2|EC873088
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|149065632|gb|EE286754.2|EE286754
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|91874476|gb|EB404433.1|EB404433
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|148933153|gb|EC876792.2|EC876792
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTTATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|76016944|gb|DT944114.1|DT944114
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|149072486|gb|EE160764.2|EE160764
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|149004888|gb|EE039399.2|EE039399
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|89762356|gb|DY689977.1|DY689977
EST:     AGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: AGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACC-ATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|91875637|gb|EB405594.1|EB405594
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|148956328|gb|EC902132.2|EC902132
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|148966764|gb|EE017849.2|EE017849
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|50326451|gb|CO521577.1|CO521577
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|60343523|gb|DN210496.1|DN210496
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|149110924|gb|EE294422.2|EE294422
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|148932453|gb|EC876177.2|EC876177
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
EST: gi|101399438|gb|EB821591.1|EB821591
EST:     TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTT                         GTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT
genomic: TAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 172

CAGCAATCTGTGGCTCTTGGCAATACGGCAAATCCAAGGGCTAGGTACTGTAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATTGTGTTGGGGCACTGAACTACAAATACTTTCTTCTGTTCCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 212

CAGCAATCTGTGGCTCTTGGCAATACGGCAAATCCAAGGGCTAGGTACTGTAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATTGTGTTGGGGCACTGAACTACAAATACTTTCTTCTGTTCCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 288

CAGCAATCTGTGGCTCTTGGCAATACGGCAAATCCAAGGGCTAGGTACTGTAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATTGTGTTGGGGCACTGAACTACAAATACTTTCTTCTGTTCCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 195

CAGCAATCTGTGGCTCTTGGCAATACGGCAAATCCAAGGGCTAGGTACTGTAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatat ... atgatttcagGTGGAAGATGTGTTCTTAAGATGGATCATCATTGTGTGTGGGTGGTTAATTGTGTTGGGGCACTGAACTACAAATACTTTCTTCTGTTCCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCAATCTGTGGCTCTTGGCAATACGGCAAATCCAAGGGCTAGGTACTGTAGGAAATGCAACCAGTTGAAGCCACCTCGGTGCCACCATTGCTCTGTTTgtaagtatatggatcagctttatgttttgccagctgtcatgaatcgactaatatcatttttgtgtgctttgcctctacatgatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC