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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG

Basic information

species Zea mays
transcript GRMZM2G421857_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 12
taatatgaaatactttgaacttctgt---tttgttgtgttgatcatttttcacattctgtctgc-tggacttcacaactaatggtgc-acttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
    |   || | ||   | |  | |   |   | ||||||||  ||||  | ||    | |   |  |  |   ||       ||| || ||||| |  ||||||||||||||||||| |||||||||||||| ||||| ||||||||| |  ||||||| || ||||||||||||||||| ||||  ||||| ||||||||| 
----acttaaaagttaagattgttataactcattcgtgttgatt-ttttgaatatctattttatgttaatattctaatgggcaatgccacatttttgttatccagGCTGAAATGCCTGCAGATAGTGGTTACCCTGCTTATTTGGCTGCAAGACTGGCATCTTTCTATGAACGTGCTGGTAAAGTAAGGTGTCTTGGAAGTCCAA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 13
--------------------------------------------------------taatatgaaatactttgaact--tctgttttgttgtgttgatcatttttca-----cattctgtctgctggacttcacaactaatggtgcacttt-----------tttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
                                                        | ||||  ||   | |    |     ||||   |       | || |  ||     |||          ||| |  |||   |    || | |||           | |||    ||||| ||||||||||| |||||||| || || || ||| | ||||||||||| || || || |||||||||||||| |||||||||||||| ||| | || |
gtgagaaagatttattttttgtgcttaaaatacatatattttgtagccttactttatgatattgaactttctttcttgactagtttaactagacaatttatataccattaggcatgagacacatgggaatggacattgatcaatgtattttgatgatattgttgtcttccacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCTTTCTATGAACGTGCTGGGAAGGTAAAATGTCTAGGAGGCCCTG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 13
-taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattc---tgtctgctggacttcacaact-aatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
 |    |    ||  | ||   | |    | |    || | |||    |||||     ||     ||  |     |  |  ||| ||  || || |||    ||||| ||||||||||| |||||||| || || || ||| | ||||||||||| || || || |||||||||||||| |||||||||||||| ||| | || |
cttgactagtgtaactagacaattta---tataccattaaccatgagacacatgggaatggacattgatcaatgtattttgatgatg--ctgttgtcttccacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCGTTCTATGAACGTGCTGGGAAGGTAAAATGTCTTGGAGGCCCTG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
------taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
      | ||  |    |||||     | ||  |  | ||||||  |   | |||| ||   | | ||    ||    ||   |  |   |||| || |     ||||||||||||||||||| ||||| || ||||| ||  | || |||||||| ||||| || ||||||||||||||||| ||||||||||| ||  | ||||
gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgtttta---tagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 13
---taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacat-tctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
   | || | | |||  |  |  || ||   | |||  ||  | || |    | | ||| | ||||     | | || | |     |  |  |||||    ||||| |||||||| || || ||||||||||| |||||  |||| |||||||| || || || ||||| ||||||||||| || || || || ||  | ||||
gcatgatttcatataactgca--ttttgaaatattgattttgtaatctgaagcgtgtctctttgcttactctgaaaattgaca--actataatttcttaatcagGCAGAAATGCCAGCAGACAGTGGTTACCCTGCTTATCTGGCAGCACGTTTAGCCTCTTTCTATGAGCGTGCTGGTAAAGTTAAGTGCCTTGGTGGGCCAG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 13
taatatgaaatactttgaacttctgttttgttgt-gttgatcatttt----tcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
   |||  | |  |||     | ||  |  || |  || | || |||    | |   |   ||| ||||  | | | | || |  ||   |  |||||     ||||||| |||||||| |||||||| || || ||||| ||||| |||||||| || || || ||||| || ||||| || || |||||||||||  | ||||
---tatttatttatttatttatttgaatcattattatttagcaatttagggttattattcatct-ctggcttactccaatattt-tgtcttaatttctcaaaaagGCTGAGATGCCTGCGGATAGTGGCTATCCTGCTTATTTGGCAGCACGTTTAGCCTCTTTCTATGAGCGCGCTGGCAAAGTGAAATGTCTGGGTGGACCAG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 13
-taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattctgtctgc--tggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
 ||   || | ||   |  | ||  | |  |    |  ||| |       |  |     |    ||   |||  |  |     || |  |  | |||   |||||||| |||||||| || |||||||||||||||||| | |||||| | || || || || |||||| | || || || || || |||||||| || ||  
ttacattgtattatccttcagttaaggtaggaacggaagatgaggaaatgctcttcagatatcatgtttttcttatttccaactgtatgtggtgctg---cagGCTGAGATGCCTGCGGACAGTGGTTACCCAGCTTACCTAGCTGCAAGATTAGCTTCTTTCTATGAAAGAGCAGGGAAAGTTAAGTGTCTGGGGAGCCCGA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------------taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
                                                   || ||| |  || ||   | || ||    ||   |       || | ||     ||||     ||||  |  ||     ||  ||| | |  |  | |||||||| ||||||||||| |||||||||||||| ||| | |||||| | ||||| |||||||||||| | || || || || |||||||||||||| ||| 
gtatgttctcaggactttcctttggtgttttttttagggtttcaaacttgttagtatcatgtattt---atttatggacagtataggcaggttttgtccatgcaatgtcattcagactctaagacatgcagt-tactctgtggttttgcagGCTGAGATGCCTGCTGACAGTGGTTACCCAGCGTACCTTGCTGCAAGGTTGGCCTCCTTTTATGAAAGAGCAGGAAAAGTGAAATGTCTGGGAAGCCCAA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 13
---taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattctgtctgctggacttcacaactaatg-gtgcacttttttctgg-tccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
   ||||||  || | | |   ||   |   |     |     || ||   | || ||   | |  ||  |     |||||  |||  |  || |  || | |||||||| ||||||||||| |||||||| ||||||||| | |||||| | || || || || |||||| | || || || || || ||||||||||| ||  
tcataatatttaaaaatatttgctcagggcata----gccagacaattcagaaatgctactttccagatattttg-ctaatatgtgatcacttgtggggcttcagGCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTAGCTTCTTTCTATGAAAGAGCCGGGAAAGTGAAGTGTCTGGGAAGCCCGA

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 12
taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
                                     |    | | | |  |||| |||       |||  || | |     | |         |  ||||| ||||||||||| || |||||||| ||||| || |||| ||||||||||||  | ||||| || || ||||| ||||| ||||| || || ||||| |
-------------------------------------gtaagtctctgattttctttcta------ttcctaatttacaa-acgcc--------gcgcagGCCGAAATGCCTGCCGACAGTGGTTATCCAGCGTATTTGGGTGCACGTTTGGCTACGTTTTACGAGCGGGCTGGAAAGGTTAAATGCCTTGGTAGTCCCG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 12
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 13
taatatgaaatactttgaacttctgttttgttgtgttgatcatttttcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
                                     |    | | | |  |||| |||       |||  || | |     | |         |  ||||| ||||||||||| || |||||||| ||||| ||  ||| ||||||||||||  | ||||| || || ||||| ||||| ||||| || || ||||| |
-------------------------------------gtaagtctctgattttctttcta------ttcctaatttacaa-acgcc--------gcgcagGCCGAAATGCCTGCCGACAGTGGTTATCCAGCGTATCTGGGTGCACGTTTGGCTACGTTTTACGAGCGGGCTGGAAAGGTTAAATGCCTTGGTAGTCCCG

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|67026160|gb|CO454909.1|CO454909
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|6637071|gb|AW261343.1|AW261343
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|31360193|gb|CD444550.1|CD444550
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGGTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|51592889|gb|CV072035.1|CV072035
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|61118945|gb|DN559906.1|DN559906
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|19437277|gb|BM953687.1|BM953687
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacattctgtctgctggacttcacaactaatggtgcacttttttctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTAAAATGTCTGGGAAGTCCAG
                          aactaat  putative branch site (score: 2)
                                       cttttttctggtcc  putative PPT
                                      actttttt  TA-rich tract