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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACTCCTCCCGCTGATGCTACCTCCAATTGGCTATGGATGCTTGCCAAAGCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTGgtatggattccagaatggactgttatatggtgaacatgcattttgagtgcattaccactgtcagtttagtcaatttatgaattaaacacctatagagtgt...

Basic information

species Zea mays
transcript GRMZM2G017616_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017616_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g08220.1 (Oryza sativa), 5'ss of exon 7
TTACTCCTCCCGCTGATGCTACCTCCAATTGGCTATGGATGCTTGCCAAAGCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTGgtatggattcca--gaatggac-tgttatatggtgaacatgcattttgagtgcattaccactgtcagtttagtcaatttatgaat-taaacacctatagagtgt----------
| || ||||||  |||||||||||| |||||||| |||||||||||||| || ||||||||||||||||| || ||||| || ||||| || |||||||||||   |    |  |||   || ||  |||  ||   ||    |     |  ||  | |||       | ||  || || ||||  |    ||  |  | ||            
TGACGCCTCCCTATGATGCTACCTCGAATTGGCTCTGGATGCTTGCCAAGGCCCATGTCAGCTCCAACGATGCTGGTGTCCATCAGCTGGTCAATCACTGgtaaaaaaaaaaaagaacaaacatgccataatgttgtcactgctgccttg-acaagaacaccaaattgtcaggtaacttctgaacattgtgactaaccgggtcctctctttcag

upper sequence: GRMZM2G017616_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv09s0002g01080.t01 (Vitis vinifera), 5'ss of exon 6
TTACTCCTCCCGCTGATGCTACCTCCAATTGGCTATGGATGCTTGCCAAAGCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTGgta--tggattccagaatggactgttatatggtgaacatgcattttgagtgcattacca-ctgtcagtttagtcaatttatgaattaaacacctatagagtgt
| || ||||| |  ||||| ||     |||||   |||| ||| || |||||||||||| |||||||||| || || ||||| || ||||||||||| |||||  | || | ||   | ||      || | | || ||    ||  |  | ||    |  | | |  || |||   | ||  |                   
TCACACCTCCGGTCGATGCAACAAGTGATTGGACTTGGAAGCTCGCAAAAGCTCATGTCTGCTCCAACGATGCAGGAGTTCATCAACTCGTTAATCATTGgtaaatagacttcacttttgatgtagttaagattaagattttattgaaacgaatactaaattatgaaattggtcttatcatatag------------------
















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|211506486|gb|FL158295.1|FL158295
EST:     CTCATGTCAGCTCCAANCGACGCCGGTGTTCACCAGCTCGTTAATCACTG                         GCTGAGGACACATGCT
genomic: CTCATGTCAGCTCCAA-CGACGCCGGTGTTCACCAGCTCGTTAATCACTGgtatggattc ... actcttgcagGCTGAGGACACATGCT
EST: gi|211506485|gb|FL158294.1|FL158294
EST:     GCTCATGTCAGCTCCACCGACGCCGGTGTTCACCAGCTCGTTAATCACTG                         GCTGGAGGAC-CATGCT
genomic: GCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTGgtatggattc ... actcttgcagGCTG-AGGACACATGCT
EST: gi|71434733|gb|DR815783.1|DR815783
EST:     GCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTG                         GCTGAGGACACATGCTGTAATGGAGCCGTTCATATTGGCAGCGCATCGGCG
genomic: GCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTGgtatggattc ... actcttgcagGCTGAGGACACATGCTGTAATGGAGCCGTTCATATTGGCAGCGCATCGGCG
EST: gi|71418314|gb|DR804399.1|DR804399
EST:     GCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTG                         GCTGAGGACACATGCTGTAATGGAGCCGTTCATATTGGCAGCGCATCGGCG
genomic: GCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTGgtatggattc ... actcttgcagGCTGAGGACACATGCTGTAATGGAGCCGTTCATATTGGCAGCGCATCGGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACTCCTCCCGCTGATGCTACCTCCAATTGGCTATGGATGCTTGCCAAAGCTCATGTCAGCTCCAACGACGCCGGTGTTCACCAGCTCGTTAATCACTGgtatggattccagaatggactgttatatggtgaacatgcattttgagtgcattaccactgtcagtttagtcaatttatgaattaaacacctatagagtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC