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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGGCCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatctcttcccctcccctcccttccgctccctcgccagctcgcgcgctctcctcgcacggcctcggccattgtcaattttgccattatcatttg...

Basic information

species Zea mays
transcript GRMZM5G845755_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 1
GATCGGCCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatctcttcccctcccctcccttccgctccctcgccagctcgcgcgctctcctcgca-cggcctcggccattgtcaattttg--ccattatcatttg
    |  ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||||| ||||  |||   | |   |||| || || | | || ||     | | |  | |  ||||  | || || ||    |||| ||| |   || | ||   ||
CCCAGATCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtgagtg-cctcccactcctacctcgctacctcgctcttgct--tccaccctgtgttgtcgcctctgcatctgcgtgggtcagtttagattcagtgtcggatg

upper sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 2
GATCGGCCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgat----ctcttcccctcccctcccttccgctccctcgccagctcgcgcgctctcctcgcacggcctcggccattgtcaattttgccattatcatttg
||  | | || |  |||||||||||| |||| ||||| || || || || |  || || || || || |||||||||||||| |||||||| |||||||||| |||       || |||   || |  || ||  ||| |||    |  ||    | ||| |    |   |   |  |  ||   | |   | | ||  |    
GACGGCCAGGTGTTATGTCCAAGGCCCGGGTTTACACAGATGTGAATGTCCAACGTCCGAAAGATTATTGGGACTACGAGGCCCTCACCGTCCAATGGGGgtaagttccatggctattcgattcactccctttatgcttcctt---aattccaatgttctacagagatatctgggcacggtgaggaatcatcgactagaaacc-

upper sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ28543 (Selaginella moellendorffii), 5'ss of exon 1
GATCGGCCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatctcttcccctcccctcccttccgctccctcgccagctcgcgcgctctcctcgcacggcctcggccattgtcaattttgccattatcatttg
|     |||||||||||||||||||| || | ||| |||| || |||||||||||||| ||||||||||||||||||||| | ||| | ||  | ||||||| ||                | |   || || |   | |   | ||  |  |||| ||      |  | ||     |                      
GTGGCCCCGGCGCCATGTCCAAGGCCCGGATATACGCCGATGTGAACGTGCTGCGCCCAAAGGAGTACTGGGACTACGAGTCTCTCTCGGTGGAGTGGGGgtgagg---------------cttttgtttcgtttttttgttggatctagatctcttcttctt--gtttgggtggcag----------------------

upper sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 1
GATCGGCCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatctcttcccctcccctcccttccgctccctcgccagctcgcgcgctctcctcgcacggcctcggccattgtcaattttgccattatcatttg
|     |||||||||||||||||||| || | ||| |||| || |||||||||||||| ||||||||||||||||||||| | ||| | ||  | ||||||| ||   | | || |  |        ||  | |   ||   | |||   |    || | |   |||                                 
GTGGCCCCGGCGCCATGTCCAAGGCCCGGATATACGCCGATGTGAACGTGCTGCGCCCAAAGGAGTACTGGGACTACGAGTCTCTCTCGGTGGAGTGGGGgtgaggcttttgtttcgttt-------ttttgttggatctagatctc-ttcttcttctttgggtggcag-------------------------------

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|149081763|gb|EE170917.2|EE170917
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|148990948|gb|EE032377.2|EE032377
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|29946904|gb|CB816382.1|CB816382
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|5268357|gb|AI770321.1|AI770321
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|149004751|gb|EE039248.2|EE039248
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|78115139|gb|DV533527.1|DV533527
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|211130017|gb|FL138061.1|FL138061
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTATTAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|149078770|gb|EE167579.2|EE167579
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|211130018|gb|FL138062.1|FL138062
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG
EST: gi|31355313|gb|CD439670.1|CD439670
EST:     CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGG                         TGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATATTT
genomic: CTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatc ... cttttttcagTGAGCAGGATAACTATGAAGTTGTTAGGAAAGTTGGGAGAGGGAAATACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCGGCCGGCGCCATGTCCAAGGCCAGGGTCTACACCGACGTCAACGTGCTGCGCCCCAAGGAGTACTGGGACTACGAGGCGCTCACCGTTCAATGGGGgtcagtgatctcttcccctcccctcccttccgctccctcgccagctcgcgcgctctcctcgcacggcctcggccattgtcaattttgccattatcatttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG