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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT

Basic information

species Zea mays
transcript GRMZM2G165418_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
-----------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgctaata-atttatattgcagaa-gttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
                                                                         | |||   |  | ||   | ||  | |||| ||   ||| |  ||     |   |||| || |  ||||     ||||| ||||||   |||  ||||||||||||||||||||||||||||||||||||||||||||||||||| || || |||||||| || |||||||| ||||||||| |||| | ||| || |||
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggct--gcataagattctctattctatactagtaatagaatgtcacaatat-cagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaa-acagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
  | |   || |||         | | |  | | |||  || | ||| || ||     | || || |  | |  |       | ||     |     |||||||||||||||| ||||| ||||| ||| |||| || || ||||| |||||||| ||||| || || ||||| |||   | | |||| | |||||| |||
ttttgcatacaaagaaaagcatttttctggatcctattatatttattcat-ttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgct------aataatttatattgcagaagttatta---tatgttttatga--gttaacaaagg---cctaaaa--acagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
                                                                         |  | |  |  |    |  || || | |  | | |  |      ||| | ||  |      |  ||| ||   ||   ||| |||    | || |  |   | | | |  |||||||||| ||||  ||||||||||| |||||||| || || ||||| || ||||| |||||||| ||||| || || |||| | |||| | ||| || |||
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaa-atgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgctaataat--ttatattgcag---aagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
                                                                     | |      ||  || |||   |   ||    | |  |    ||  |||| | | |    || || | ||||  ||| | | |   ||   |   |   |||| ||||||||||  || ||| ||   |||||||| || |||||||| || ||||| ||||||||||||||||||||||||| | |||| | | || | |||
gtgagtgatcttttggtctttgtctagttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatgtggaattttaatttctgatattctttttaaatgctcatttgatcat--acagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatat-gctaataatttatattgcagaagttattatatgttttatgagttaacaaagg--cctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
        |  | ||    ||   |   | | ||| | |    |||    | ||    |   |  | | |  |  || ||| |   |  |  | |  |  ||| ||||||||||| || |||||||| |||||||| || || ||||| || ||||| |||||||| || || || ||||| | | |||| | || ||| || 
-tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttag--tgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 8
cctagacaactaaggc--tgtagcctatgtata-acatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
  || |  |||| |    | |||  | | | |  |   |   | ||  |    | |    ||||  |||   |      |  ||   || |     ||  ||| ||||||||   |||  | |||||| | || || || || ||||| |||||||| |||||||||||||| |||||| ||||   ||||   || ||||| 
gatatattactaggatgatttagaatttttctgtatccagaatgatcttaccaagtttgcaagtacttaagggacagtcgtattgttaatga---gaattcagGTTTGAGGAGACTGAGCCTCCTGGAGCTAGGTCGTTTTTCACAGAGATTATTGCTTCAATTTCTGATATCAAGTTTGCAAGAGGTGGCCGGTACATTCTG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcct-----aaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
          |    ||  |   ||| | |     ||| | |||  || | ||     | |  |  | |  | |   |  |   |  | | |          ||| ||||||||   |||     |||||||||||||||| ||||||||||| || || || ||||||||||| |||||| | ||    ||    || ||||| 
-----tgcgtttttcctaaaagttatatttccacaatggttataggttgtgttttctgaatattggtttcatattgaaacttgtattgtctttttgtgggtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTG

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 8
-cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgtttta--tgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
    ||  |||| |   |  |     | | |  || ||| | ||  | | ||  |  ||  |  || |  |||  |  |    |   |  |   |     ||| ||||||||   |||  |  |||||||||| || || || |||||||| ||||| ||||||||||| || |||||| ||||   ||     |||||||| 
gttgagggaactgatcattcactggttatgtccca-atgttgatg-tatgtac-gaggatatgctttttcgttgaagtttgcatggtattgatgtggttgcagGTTTGAGGAGACTGATCCCTCTGGATCAAGGTCTTTTTTCACAGAAATCATTGCTTCAATTTCTGACATTAAGTTTGCAAGAGGTGATCGGTATATTCTC

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaa-----ggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
   ||| |  |   |   | || |     |  |   | |  |  | | || ||| | || || |  | |  |  | |    | || |       | |     ||| ||||||||  ||||  |  ||||| | || || || || |||||||||||||| ||||||||||| || |||||| ||||   |||    || ||||| 
--aagatatttctaga-atggcttggaagtttccactaccta-gagtgatcttg-ataaattttcttgtagtaaaaggacaaccatattcggaacttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTATTGCTTCAATTTCTGACATCAAGTTTGCAAGAGGTGGTCGGTACATTCTA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
                                               ||  ||   |   |       ||   |   ||||  | |       ||   || || |||||||| ||||| |||| | ||||||| || |||||||||||| |||| || || || ||||| ||||||||  | | |||    || ||||| 
----------------------------------------------gtaagttcttgtcttctacgcctggactg-aagtt--ccatccttccaatgtagGTTCGAGGAACAGGAAGCTCCTGCAACAAGATCATTTTTTACAGAAATTGTTGCCTCCATCTCGGATATCAAGTTTTCTCGTAGTGGACGGTACATTCTC

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
                                               ||  ||   |    |  ||   ||    |||  |  ||     | ||    || || |||||||| ||||| |||| | ||||||| || |||||||||||| |||| || || || ||||| ||||||||  | | |||    || ||||| 
----------------------------------------------gtaagttcttg--tcttctacgcgtggactgaagttccatccttccaatg-tagGTTCGAGGAACAGGAAGCTCCTGCAACAAGATCATTTTTTACAGAAATTGTTGCCTCCATCTCGGATATCAAGTTTTCTCGTAGTGGACGGTACATTCTC

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|31352864|gb|CD437221.1|CD437221
EST:     CGACTTATTGATCTGCGCCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|211384024|gb|FL015619.1|FL015619
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|211386654|gb|FL015627.1|FL015627
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|211386649|gb|FL015622.1|FL015622
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
                                           gcctaaa  putative branch site (score: 3)
               ttattatatgttttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA