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

gtcagctgcttgctcgctggcactcccatcccatgcaccagccaccacctctgttgatgacttgattcctaattaattaccttggcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG

Basic information

species Zea mays
transcript GRMZM2G070605_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070605_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g13770.1 (Oryza sativa), 3'ss of exon 1
--------gtcagctgcttgctcgctggcactcccatcccatgcaccagccaccacctctgttgatgacttgattcctaattaattaccttggcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG
        |   |     ||||    |  | ||  |  |    ||      |  |  |   |   |||  |||||  |  ||  ||   ||||       ||||| || ||| | | ||| ||||||||||||||||| ||| || |||| ||||||||||||||||||||
ttccactggagtgtgatatgcttatggttaatcggaatcagctcagagattattaatttattatttga--tgatttttgtttttttgatttggttttgctagGGAAGCGAAGCCAGCGGGGTTCCTGGAGAAGTACCCTGCCTTGATCACCGGCTTCTTCTTCTTCATGTG

upper sequence: GRMZM2G070605_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15759 (Selaginella moellendorffii), 3'ss of exon 1
----gtc-agctgcttgctcgctggcactcccatcccatgcaccagccaccacctctgttgatgacttgattcctaatt--aat----taccttgg-cgacagcagGGAGGCCAAGTCTGTGG---------GTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG
    ||| |   |     |    |    |||   |   |  |   |  |  | || || |  | |||| |    ||  |  |||    | | |||| |  |  | | || || |||  ||| |         | ||   |||||| |||||||| || |||||||| ||||||||||| |||||
gtaagtcgaatcgagattttagagattttccttccttttctagatgggaggagctttgctcgttactttacctttacctggaatgcggtgctttggacagCTCCGGCGATGCAAAGATTGTCGAGGCGTCTGGATTTGCGGAGAAATACCCGGCTCTCGTCACTGGATTCTTCTTCTTTATGTG
















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|76914837|gb|DV165713.1|DV165713
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149013546|gb|EE043037.2|EE043037
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|101394747|gb|EB819306.1|EB819306
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|148966890|gb|EE018012.2|EE018012
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|148986357|gb|EE030094.2|EE030094
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149000807|gb|EE038032.2|EE038032
EST:     TCGCAGGGCGCCAGGAGGCACACGCCATGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAGGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149075125|gb|EE163618.2|EE163618
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|211407726|gb|FL367074.1|FL367074
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149112153|gb|EE191267.2|EE191267
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149026859|gb|EE046212.2|EE046212
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149097452|gb|EE183315.2|EE183315
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149095141|gb|EE180755.2|EE180755
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149015293|gb|EE045098.2|EE045098
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|71766326|gb|DR964263.1|DR964263
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCTTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|211475706|gb|FL352571.1|FL352571
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|149075192|gb|EE163691.2|EE163691
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
EST: gi|78077772|gb|DV506204.1|DV506204
EST:     TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGG                         GGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG
genomic: TCGCAGGGCGCCAGGAGGCACACGCCACGGCGGCCCGCCGCAGCCGCAGGgtcagctgct ... gcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccaccacctctgttgatgacttgattcctaattaattaccttggcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG
                         attcctaattaatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagctgcttgctcgctggcactcccatcccatgcaccagccaccacctctgttgatgacttgattcctaattaattaccttggcgacagcagGGAGGCCAAGTCTGTGGGTTTCCTGGAGAAGTACCCGGCCCTGGTCACTGGCTTCTTCTTCTTCATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT