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

gtgagcgatccgtcctcccagatcccgctctgatctagggcgggcttgagtgtcccgtgctgatttggcgttccgtggcggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCACCCGCGTGGCGATGGCGTGTTCTGTGCCTTCCCCAACGGCTGCAG

Basic information

species Zea mays
transcript GRMZM2G011364_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011364_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g39650.1 (Oryza sativa), 3'ss of exon 1
gtgagcgatccgtcctcccagatcccgctctgat-ctagggcgggcttgag--tgtcccgtgctgatttggcgttcc-----gtggcggtggg-----------cagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCACCCGCGTGGCGATGGCGTGTTCTGTGCCTTCCCCAACGGCTGCAG
||||||||||||   ||       ||||     | | | | ||  || ||    ||||||||||||| || |||| |     |||| ||||||           |||||| |   | ||   |  |||||| ||||||||||||| |||| |||||||||||| ||||| |||||  |||| || |||||||| ||||||||
gtgagcgatccggtttcttcatctccgccagatttccacgccgatctcgatctcgtcccgtgctgatctgacgttgctggtggtgggggtgggggtggggagtgcagGTGTTGAGGATGGGGACGGAGGAGCAGGTGCCGTACAGGATGGGCGTCCACCCGCGCGGCGACGGCGTCCTCTGCGCATTCCCCAATGGCTGCAG
















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|71434096|gb|DR815146.1|DR815146
EST:     GGCCCTCGCCACCGGGGAAGAGGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCA
genomic: GGCCCTCGCCACCGGGGAAGAGG-CCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGG-TGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCA
EST: gi|149014922|gb|EE044651.2|EE044651
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
EST: gi|149096646|gb|EE182411.2|EE182411
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
EST: gi|78081364|gb|DV509776.1|DV509776
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
EST: gi|149070573|gb|EE158979.2|EE158979
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
EST: gi|74244209|gb|DT652123.1|DT652123
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
EST: gi|93284045|gb|EB676309.1|EB676309
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGGGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
EST: gi|76929908|gb|DV172213.1|DV172213
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
EST: gi|76012351|gb|DT939521.1|DT939521
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGCCGAGGTGAATAGCGAGGAGGAGGTGCCGTACAGAATGGCC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCC
EST: gi|148965898|gb|EE016799.2|EE016799
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
EST: gi|78083929|gb|DV512322.1|DV512322
EST:     CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACG                         GTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC
genomic: CGGCCCTCGCCACCGGGGAAGAGGCCGCGCCGGCTCTCTCCCCCGATACGgtgagcgatc ... cggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagggcgggcttgagtgtcccgtgctgatttggcgttccgtggcggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCACCCGCGTGGCGATGGCGTGTTCTGTGCCTTCCCCAACGGCTGCAG
                        tgctgat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgatccgtcctcccagatcccgctctgatctagggcgggcttgagtgtcccgtgctgatttggcgttccgtggcggtgggcagGTGGTCGAGGTGAATAGTGAGGAGGAGGTGCCGTACAGAATGGCCGTCCACCCGCGTGGCGATGGCGTGTTCTGTGCCTTCCCCAACGGCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG