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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttcttgaccctgtacaatagttcttgatcctgtgatttagttcttgaccctgtgatatgtggcattgtctaaagtttctttcttttatcttactgcagACAGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT

Basic information

species Zea mays
transcript GRMZM2G097502_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 8
------------ggttcttgaccctgtacaatagttcttgatcctgtgatttagttcttgaccctgtgatatgtggcattg-tctaaagtttctttcttttatcttactgcagACAGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
             ||      |   | | ||   ||| | ||  |  |  |||   | | |   | |    |||| || || | || |   |||| ||  ||||| |||||||||||||||| |||||||||||| || |||||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| | |||
gtataattttattgtcacgttcttcgcaaaaggcttcataattattagcatta---cataattatatttgttgtgacaatgatatagaagctcttgctactatctgactgcagACAGTGAAGCGCCACAAGAACCAGCTAAACACCACAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCAAATATCATCAATCAGATTGATACTCT

upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G38370.1 (Glycine max), 3'ss of exon 7
ggttcttgaccctgtacaata---gttcttgatcctgtgatttagttcttgaccctgtgatatgtggcat-tgtctaaagtttctttcttttatcttactgcagACAGTGAAGAGCCACAA---GAACCTGCCAAACACCATAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
   |    |    | | ||     |||  |  ||   |||| |  |   |||       ||||   ||||   | ||| |||  ||     |      |||||||        | |||      | ||     |   | |   | |||||||| || ||||||||||| ||||||||||| |||||  |   ||| ||||| |    
--attagaaaggagaaaaaggtgtgtttatattctcatgatctcatcaatgaaatct--atattctgcatacctgtaatgttgtttatccatgggcacctgcagATGACCCCAAACCATTCATTGGACGCATGAGCAATCGCCAAAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC---

upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G16680.1 (Glycine max), 3'ss of exon 6
---------ggttcttgaccctgtacaatagttcttgatcctgtgatttagttcttgaccctgtg-atatgtggcattgtctaaagtttctttcttttatcttactgcagAC-AGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
         ||     ||   |||  |    ||| ||||| | | | | |  |||  |  ||| | |  |||    |||| ||    |     | |  |  | ||  || || | | |   | |||| ||      ||| | |||    |||||||| || ||||||||||| ||||||||||| |||||  |   ||| ||||| |    
ggagtgggaggggtgggattatgtttatattttcatgatcttatcaatgaaatctatattctgcgtacctgtaatgttgtttatccatgggcacctgcagATGACCACAAACCATTCATTGGACACATGAG-----CAATCGCCA---AAGATTGGGCCCTGCAGGCCTTGCTTTGCATTATGCAAATATAGTGCTTCAAATTGATAC---

upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G33040.1 (Glycine max), 3'ss of exon 7
ggttcttgaccctgtacaatagttcttgatcctgtgatttagttcttgaccctgtgatatgtggcattgtc-taaagtttctttcttttatcttactgcagACAGTGAAGAGCCACAAG---AACCTGCCAAACACCATAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
||      |   |  |    | ||  | |||   | | |   | |   |  ||||| | |    |||  |  ||| | |  ||     |   |  |||||||     |  | |||  |    || |   ||     |   | | |||||| || ||||||||||| |||||||||||||||||  |    || ||||| |    
gggagggaaagattaatctgattttctcatcaaattactct-tccaaaaagctgtgtttttgttcatgattgtaatggtgtttatccgtgggtacctgcagATGACCATAAACCATTAATTCAAACCATCAGCAGTCGCCAAAAATTGGGTCCTGCAGGCCTTGCTTTGCATTATGCTAATATAGTGCTCCAAATTGATAC---

upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0031g02970.t01 (Vitis vinifera), 3'ss of exon 7
ggttcttgaccctgtacaatagt-tcttgatcctgt-gatttagttcttgaccct-----gtgatatgtggcattgtctaaagtttctttcttttatcttactgcagACAGTGAAGAGCC---ACAAGAACCTGCCAAACACCATAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
     ||| || |    || ||  ||| | |  |||  ||  ||    ||   ||       || ||  |||||    ||| ||||| || |     |   ||||||| |||||    ||   | | | | |||  |   | ||| | ||||||||||| || || ||||||||||||||||| |||||  | |  || |||||      
-----ttgtccttacctaaaaggatctaggtaatgtcaatagagccagtggttcttataaaagaaataaggcatctgataatgtttccttat--gggcaacctgcagATAGTGATACACCTGTAAATGGATCTGTGAGTGATCATCAAAGATTGGGACCTGCTGGTCTTGCATTGCATTATGCAAATATTGTTATGCAAATTGATGC---

upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S54_228V6.1 (Physcomitrella patens), 3'ss of exon 7
--ggttcttgaccctgtacaatagtt--cttgatcctgtgatttagttcttgaccctgtgatatgtggcattgtctaaagtttctttcttttatcttactgcagACAGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGA---TTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
     ||      | |  || || |   ||  || |    | | |    |  |    ||  ||||  | ||| | |||  | |   | |     | | | |       |||  ||||  | ||    |  |||    ||  | ||   ||||| ||| | ||  | ||  |||||||||||||||||||||||||||||||      
ccatctcagtgtgcagctcattaatatactaaatacaagcagtcaaaaatctagaa-gtagtatggtgaattttataacatatacatgtggctgcatgcagTGTTTCTTGAGAAGCCTGAGGAGGAGGAAAAAAGAAATGCTGGAAAATTGGGTCCATCGGGTTTGGCCCTGCATTATGCTAATATCATCAATCAGATTGA------

upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S15_33V6.1 (Physcomitrella patens), 3'ss of exon 8
-----ggttcttgaccctgtacaatagttcttgatcctgtgatttagttcttgaccctgtgatatgtggcattgtctaaagtttctttcttttatcttactgcagACAGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGA---TTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
      |  |      || | || |||    | |   |   |     | |    |     ||  |||||||   | || |       | |         | |||     ||| | |||  | |||   || |||    ||  | ||    ||||| || | ||| | ||  | ||||||||||||||||||||||| |||||      
gggtcagcacagtttgcttttcattagcagataa--gtacaaacggttgcacatctagaggacgtgtggcaaattttataacacacgtgtggctatacgcagCATTTCTTGAGGCGCCTGAGGAAGAGGCAAAAAGGAATGCTGGAAAGCTGGGATCATCGGGCTTGGCCCTCCATTATGCTAATATCATCAATCAAATTGA------

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|78090767|gb|DV519141.1|DV519141
EST:     TATTGTCCACTTCTTATATTTGGAGATATATAATGCCTTCGGTCGTCCTG                         ACAGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGATTGGGACCAG
genomic: TATTGTCCACTTCTTATATTTGGAGATATATAATGCCTTCGGTCGTCCTGgtataatcct ... cttactgcagACAGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGATTGGGACCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaccctgtgatatgtggcattgtctaaagtttctttcttttatcttactgcagACAGTGAAGAGCCACAAGAACCTGCCAAACACCATAATAGATTGGGACCAGCAGGCCTTGCATTGCATTATGCTAATATCATCAATCAGATTGACAATCT
                                           atcttac  putative branch site (score: 3)
                               tttctttcttttatct  CT-rich tract
                               tttctttcttttat  TA-rich tract