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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatttgcaaccttaacttagtagatcattttatcttttgaacgaaatgtatttgtgttcaaatcagcttgtgataagcatatctttatttgctt...

Basic information

species Zea mays
transcript GRMZM2G366935_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G366935_T09 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g40840.1 (Oryza sativa), 5'ss of exon 10
GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttat----ttgcaaccttaacttagtagatcattttatcttttgaacgaaatgtat-ttgtgttcaaatcagcttgtgataagcatatctttatttgctt
||||||||||||||||| ||||||||||| || || ||| |||||||||||||||| |||||||| || || ||||| || |||||| ||||| | ||||   || |     ||    |   |||| |  ||||||||| | ||   | |    | | | ||||  ||||   |||  ||  ||| |  |||| | |||    
GGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAGgtacattgtggcagtgtgcacactactttgatgatcattttctttt---acctttttctgtgttgtcctcaatatagcaagtagtaaacgaatctatgtttta--

upper sequence: GRMZM2G366935_T09 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA06G08480.2 (Glycine max), 5'ss of exon 9
GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgt------tatttgcaaccttaacttagtagatcattttatcttt---tgaacgaaatgtatttgtgttcaaa----tcagcttgtga-taagcatatctttatttgctt----------------------------------------------------------------
|| ||||||||||||||||| ||||| ||  |||| ||||| ||||||||||| ||||||||||||||| | ||||||||||||||  | |  || | ||  ||      | | |  ||| ||   | | |    | |   |  |||   |||   | ||  |   |  ||| ||    | ||    ||| |  | |   |   |  || ||                                                                
GGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAAgtaagtagtgaatttatagaacattctttaaatttcccctgccagttttgtttgaggtacatcaagaggccttccaagttatgagtcaatgactgggaaagccaaaagctgattggttatcactgaatatactaaatgtagtaacttcttttttattcatttgctcttcaatacatag

upper sequence: GRMZM2G366935_T09 (Zea mays), 5'ss of exon 9
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 10
GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgt--gtgttatttgcaaccttaac--ttagtagatcattttatcttttgaacgaaatg-tatttgtgttcaaatcagcttgtgataagcatatctttatttgctt
|| |||||||| |||||||||||||||||  |||| ||  | || ||||||||||| || ||||||||||| |||||||||||||| ||||   ||||||  || || ||||  |   | |   | || | |   ||  |||| ||| |  | ||| ||  | | |  || |    |||      ||  ||  | |   |   
GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAGgtaagttttctttgtgaagattatggtaaggaaacggttccatctgttggaaaagatggtacatatataaaagttg--ttgaacattgctaattctaaaagg---

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|71426269|gb|DR807319.1|DR807319
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGTTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|71766680|gb|DR964617.1|DR964617
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|76915207|gb|DV165881.1|DV165881
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|71760328|gb|DR958265.1|DR958265
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|24765506|gb|CA400665.1|CA400665
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAAGCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|74242829|gb|DT650743.1|DT650743
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
EST: gi|71775054|gb|DR972932.1|DR972932
EST:     ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG                         TTCTTCTGTTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA
genomic: ATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatt ... gaatatgtagTTCTTCTGCTCAGAAATATTTCAGGAGGGCAACACGTTTAAATTGGCCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAGgtgtgttatttgcaaccttaacttagtagatcattttatcttttgaacgaaatgtatttgtgttcaaatcagcttgtgataagcatatctttatttgctt

- - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacgaaa