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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaaggtattgttttttactgttgattacctgtattggatattaacagtcgattaagctatatttatgtggttgcttagtgcaacagtgcttga...

Basic information

species Zea mays
transcript GRMZM2G069765_T05
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069765_T05 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 5'ss of exon 11
GCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaaggtattgttt---tttactgttg-attacctgtattggatattaacagtcgattaagctatatttatgtggttgcttagt-gcaacagtgcttga-------------------------------------------------------------------------------------------------
           ||||||||| ||||||||  | ||||||||||| ||||| |||||||||||||||||| |||||||||||||||||||||||||||||||||| ||||||||| | |||     || | ||   |||    | |   |  ||| ||     ||     |||   | ||| |||| || | | |    ||  | |                                                                                                 
-----------TTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTGACTGTATCAGCAGCACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTAGAAAAGgtactttttcagcatatttttatgttagtgatttaaaaggttagcaaagtgttc--tcataaagaggtgcttgcctatttgtatgtttgtctaagtcattcatcaatgcagcattcattagtttttttaatggctactttctgttttgtgactatgttatatcttatttatattttgtttgtttggatcag

upper sequence: GRMZM2G069765_T05 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA20G35760.1 (Glycine max), 5'ss of exon 8
GCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaaggt-attgt--tttttactgttgattacctgtattggatattaacagtcgattaa--gctata-tttatgtggttgcttagtgcaaca-----gtgcttga----------
             | |||||| |||||||  |||||||||| || ||||| ||| ||||| ||||||||||||||||||| |||||||| || ||| ||||| |  | ||||| | |||  |  | | |||   |    ||  |   |  |  |   | |  | |  ||  ||  |||  | | | || | |   |       || ||||           
-----------AATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGAGTTCATCTGTTCAAGGTATACAGAAGgtgagtgtaatactcattgtctgtactttgcctactagttctattattgtctcatggcagtagcttacattgattctcattttcatgttcatgttcttgttgatgaacag

upper sequence: GRMZM2G069765_T05 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 11
GCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaaggtat---tgttttttactgttgattacctgtattggatattaac-agtcgattaagctatatttatgtggttgcttagtgcaacagtgcttga----------------------------------
           | | ||||||||||||||  ||||||||||||| ||||||||| |||| || |||||  |  |||| || |||||||| ||  |||| ||  | || |||||     |  ||| ||      | || | ||| |   | |||    || | || |   ||  |  |    |  |||     |  ||   || |                                  
-----------TATAAAAAATCCAAAACTTGTTCCTGGAGGTGGTGCTACAGAGTTGACAGTGTCAGCTGCCTTGAAACAGAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtagtttctatgaaccagtagcagtactactttttatttggtggtttgatggattctagttctatctcttgtccgagtagcagtttacactgattctcacttaagtgttgttgactgacag

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|149105497|gb|EE291022.2|EE291022
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTGGAAAAG               
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTC------A-GT-T-G--AAGgtgtggaaaa ...
EST: gi|87153540|gb|DY398329.1|DY398329
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTGGAAAAG               
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTC------A-GT-T-G--AAGgtgtggaaaa ...
EST: gi|211183836|gb|FL001293.1|FL001293
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAG                         TGGCCCTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTG
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaa ... tttatgtcagTGGCCCTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTG
EST: gi|60339469|gb|DN206442.1|DN206442
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAG                         TGGCCCTATGAAGCTGCTGCTCTAGCTTTTGAGGCAATTCCAAGGACTTTG
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaa ... tttatgtcagTGGCCCTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTG
EST: gi|33093954|gb|CF053948.1|CF053948
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTGGAAAAG               
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTC------A-GT-T-G--AAGgtgtggaaaa ...
EST: gi|32932271|gb|CF037083.1|CF037083
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTGGAAAAG               
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTC------A-GT-T-G--AAGgtgtggaaaa ...
EST: gi|32934718|gb|CF039530.1|CF039530
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTGGAAAAG               
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTC------A-GT-T-G--AAGgtgtggaaaa ...
EST: gi|22545904|gb|BU098263.1|BU098263
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAG                         G
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaa ... tttatgtcag-
EST: gi|22545904|gb|BU098263.1|BU098263
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAG                         G
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaa ... tttatgtcag-
EST: gi|211183835|gb|FL001292.1|FL001292
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAG                         TGGCCCTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTG
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaa ... tttatgtcagTGGCCCTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTG
EST: gi|78083039|gb|DV511432.1|DV511432
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTGGAAAAG               
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTC------A-GT-T-G--AAGgtgtggaaaa ...
EST: gi|32910520|gb|CF015332.1|CF015332
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTGGAAAAG               
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTC------A-GT-T-G--AAGgtgtggaaaa ...
EST: gi|33093289|gb|CF053283.1|CF053283
EST:     AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGGTGTGGAAAAG               
genomic: AGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTC------A-GT-T-G--AAGgtgtggaaaa ...

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGAGTTCTTCAGTTGAAGgtgtggaaaaggtattgttttttactgttgattacctgtattggatattaacagtcgattaagctatatttatgtggttgcttagtgcaacagtgcttga

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG