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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCACCGCCGCAGACGAGTTCGTGAAGGGCCGCGTCTTCCCCAACGGCGTCGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatggacctccagctcttatttgacctccgaggaccctctggccagggatctcaataaataaacttagtcgggtacttttttccgcaatctatac...

Basic information

species Zea mays
transcript GRMZM2G047564_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047564_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g39344.3 (Oryza sativa), 5'ss of exon 1
GCCACCGCCGCAGACGAGTTCGTGAAGGGCCGCGTCTTCCCCAACGGCGTCGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggat-ggacctccagctcttatttgacctccgaggaccctctggccagggatctcaataaataaacttagtcgggtactttt---ttccgcaatctatac-
||| ||||||| || |||||||||||||||||||||  |||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||||| | |  ||||   ||||   |    |||      | ||||  |      ||||  |   |   | || | ||||   |     |   || | |    | 
GCCGCCGCCGCGGAGGAGTTCGTGAAGGGCCGCGTCACCCCCAACGGCGTCGCCGTCATCACCCTCGACCGCCCCAAGGCCCTCAACGCCATGAACCTCGgtgagggtcgctcctctctctctctctctctctct-----ctctctctctctctctctctcttcctcctcctatttgggttactgggagtagggcgaccgggccg

upper sequence: GRMZM2G047564_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G35260.1 (Glycine max), 5'ss of exon 1
GCCACCGCCGCAGACGAGTTCGTGAAGGGCCGCGTCTTCCCCAACGGCGTCGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatggacctccagctcttatttgacctccgaggaccctctggccagggatctcaataaataaacttagtcgggtacttttttccgcaatctatac-
 || |    || || || || |||||||||   ||    |  ||||||||||| |||||||| ||||| || ||||| || ||||||||||||||||| |||          || |  || ||   | |  |  |    |  |   |    | ||     |     |  ||  |  || |  |         |  |  || 
TCCGCTATGGCCGAAGAATTTGTGAAGGGCACTGTTCATCAAAACGGCGTCGCTGTCATCACCCTCGATCGCCCCAAAGCTCTCAACGCCATGAACCTAGgtttttcattttcttcttcttttccataat-tatgcatgctattaagttgagaattgtgttcggagattttcttttggaatctggactgtttagttgaact

upper sequence: GRMZM2G047564_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G04460.1 (Glycine max), 5'ss of exon 1
GCCACCGCCGCAGACGAGTTCGTGAAGGGCCGCGTCTTCCCCAACGGCGTCGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatggacctccagctcttatttgacctccgaggaccctctggccagggatctcaataaataaacttagtcgggtacttttttccgcaatctatac--------------
 || |    || || || || |||||||||   ||    |  ||||||||||| ||||| || ||||| || ||||| || ||||||||||||||||| |||           ||||  |  |  ||    ||||           || |      | | |  | ||   |  ||||  | ||  ||  | |||||  ||              
TCCGCTATGGCCGAAGAATTTGTGAAGGGCTCTGTTCATCAAAACGGCGTCGCTGTCATAACCCTCGATCGCCCCAAAGCTCTCAACGCCATGAACCTAGgt---------tttccatattcttcttcgtttccgtaattatgtatgcta-----ttaagttgagaattgtcttcggagatttgcttttggaatctggactgttttgttgaact

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|211063911|gb|FL196775.1|FL196775
EST:     CGCCGTCATAACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCG                         AAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
genomic: CGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatgg ... atgattgcagAAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
EST: gi|211180614|gb|FL196781.1|FL196781
EST:     CGCCGTCATAACGCTCGACCGACCCAAGGCCCTCAACGCAATGAACCTCG                         AAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
genomic: CGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatgg ... atgattgcagAAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
EST: gi|149055220|gb|EE156145.2|EE156145
EST:     CGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCG                         AAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
genomic: CGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatgg ... atgattgcagAAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
EST: gi|211063903|gb|FL196767.1|FL196767
EST:     CGCCGTCATAACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCG                         AAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
genomic: CGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatgg ... atgattgcagAAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
EST: gi|211180621|gb|FL196788.1|FL196788
EST:     CGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCG                         AAATGGATGTTAGATACAAGGNACTTCTTGATGAATGGGAAACAAATCC
genomic: CGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatgg ... atgattgcagAAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCC
EST: gi|211180619|gb|FL196786.1|FL196786
EST:     GCSK-CAATAACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCG                         AAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA
genomic: GCCGTCA-TCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatgg ... atgattgcagAAATGGATGTTAGATACAAGGCACTTCTTGATGAATGGGAAACAAATCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCACCGCCGCAGACGAGTTCGTGAAGGGCCGCGTCTTCCCCAACGGCGTCGCCGTCATCACGCTCGACCGACCCAAGGCCCTCAACGCCATGAACCTCGgtgaggatggacctccagctcttatttgacctccgaggaccctctggccagggatctcaataaataaacttagtcgggtacttttttccgcaatctatac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaac