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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgattattttgtgccagtaacttcttttattttatttacctgcctggaaaagtgtaactgaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT

Basic information

species Zea mays
transcript GRMZM2G180720_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 2
gtgagttgattattttgtgccagtaacttcttttat-tttatt-tacctgcctggaaaagtgtaactgaatttggtgattaac-tgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
|||||| || | |||| |    | || |  || ||| |||  | | ||||| |||  |||  | | ||| |||||  |||  | |  |||||||||||||||| ||||||||||| ||||||||||| |||||||| ||||| || || |||||||||||||||||||| || ||||| ||||| |||||||
gtgagtggaatctttt-tcttggcaattatttgtatatttgctgtgcctgcttgggcaagcatgattgattttggctattttccttttgaagGTTGCTGTGGCTCATACAATTGGGCATGTTGCTGCGACAGTGAGTATGTCAAAAGTAGCAGTGTCATTCACACACATTATCAAAAGTGCAGAGCCTGCAT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G38830.1 (Glycine max), 3'ss of exon 1
---------gtgagttgattattttgtgccagtaacttcttttattttatttacctgcctggaaaagtgtaactg--aatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
         || |   |||||    ||   || ||      |  |      |   || |    |      ||  |  ||||||    ||      || |||| || |||   ||||||||||| |||||||| ||||| ||||| ||||| || || ||||| ||||| || ||||| || || || |||||||||||||
ggcaaaatagtaaagagattagggggtaaaagaaatcataatcgtcaagcattaatgtcaattagtactcaatggggaatttgaaactttgggagtgcagGTCGCGGTGTTACATACAATTGGGCATGTTGCAGCTACGGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAACCTGCAT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 1
---------gtgagttgattattttgtgccagtaacttcttttattttatttacctgcctggaaaagtgtaact---gaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
          |  | || | |  | |||  ||| | || |    |          ||  ||   |    | |||   ||| ||    |||   |  || ||||||| ||||| || |||||||| ||||||||||| || ||||||||||| ||||| || || |||||||| ||||| || || || | ||| || || |
gcaatgcatttatggtggtcaaatggtgtgagtgagtt-tgaagtaaggaaaggttgattgagtagtactcacttgagaaatttcaaattttattgtgcagGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 1
-----gtgagttgattattttgtgccagtaacttcttttattttatttac---ctgcctggaaaagtgtaact---gaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
       | ||| ||  |  |      ||   |   |||    ||   |     ||  |    |    | |||   ||| ||    |||   |  || ||||||| ||||| || |||||||| ||||||||||| || ||||||||||| ||||| || || |||||||| ||||| || || || | ||| || || |
aagtaacgcgtttatggtggtcaaatggtgggtgagtttgaagtaaggaaaggttgatttagtagtactcactaaagaaatttcaaatttttttgtgcagGTTGCGGTGGCACACACAATTGGGCATGTTGCTGCAACTGTGAGCATGTCCAAGGTTGCTGTTTCATTCACTCACATCATCAAGAGTGGAGAGCCAGCTT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 2
--------------gtgagttgattattttgtgccagtaacttcttttatt-ttatttacctgcctggaaaagtgtaactgaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
              || | ||||| | |||  |||| |  || |||||||| | || |   ||  ||||  |        |  || | |   |  ||  |  |||||||||| || ||||||||||| ||||| || || ||||| |||||||| || || || || |||||||||||||| || || || |  |||||||| |
gttgtttcaaaaaagtta-ttgatcaattta-gccatt--ctccttttattatcatatttttgaatggatgatgactttagttttcgttttatttctccttcagGTTGCTGTTGCACATACAATTGGACATGTAGCGGCAACAGTTAGCATGTCAAAAGTTGCGGTATCATTCACACACATTATCAAGAGTGGTGAACCTGCTT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G01890.1 (Glycine max), 3'ss of exon 1
---------gtgagttgattattttgtgccagtaacttcttttattt--tatttacctgcctggaaaagtgtaactgaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
         ||||   |||||    ||   || || |    |  |     ||| | ||   |  | |  | |     ||||||    ||      || ||||||| |||   ||||||||||| |||||||| ||||| ||||| ||||| || || ||||| ||||| || ||||| || || || ||||| |||||||
tacaaaatagtgaagagattagggggtaaaagaaattataatagtcaaacattaatctcaattaatacttattgggaaatttgaaattttgggagtgcagGTTGCGGTGTTACATACAATTGGGCATGTTGCAGCTACCGTGAGTATGTCCAAAGTTGCAGTTTCATTTACCCACATCATCAAGAGTGCAGAGCCTGCAT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgagttgattattttg-tgccagtaacttcttttatttta-----tttacctgcctggaaaagtgta--actgaatttggt----gattaactg-atgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
    ||  ||||| | | | | ||||  |  || || ||||     || | ||   ||  |   |||   ||||||  ||||    | | || || ||  ||||||||||||| || |||||||| ||||| ||||| || ||||| ||||| ||||| || || || ||||| ||||| || || || |  |||||||| |
-cttgtc-attatatagcttctagtatttcattctagtttaaagtattgaactttttgatattttgttgtactgaaagtggtttatgttgaattgcatatagGTTGCTGTGGCACACACAATTGGTCATGTGGCTGCAACGGTGAGTATGTCAAAGGTTGCTGTTTCTTTCACTCACATCATCAAGAGTGGTGAACCTGCGT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G03950.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtgagttgattattttgtgccagtaacttcttttattttatttacctgcctggaaaagtgtaactgaatt-tggtgatta-actgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATA--ATTAAAAGCGCAGAACCTGCAT
           ||| |||  | ||||||     |  || |||||   || | |         | |    || ||||| ||  || |||||    |  |  |||| ||| |||||||||||||||| |||||||  || | |||||| |||||||| || | |||||| |||||||||| |  || ||||||   ||  | ||  
tcttgctttaggtgtgtt--tgattttgaaagggacacgtctttagattaagtgtgtaagtagtattgatggaactgtatgatgatgattttgattgttcagGTGGCTTTGGCGCATACAATTGGACATGTTGAAGCGATAGTGAGTATGTCTAAAGTAGTAGTGTCCTTCACACACACATCATCAAAAGCAGTGAGGCAGC--

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 1
gtgagttgattattttgtgccagtaacttcttttattttatttacctgcctggaaaagtgtaactg-aatttggtgattaa-ctgat----------gaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
 | | |||    |  | |   | |   |||  ||| |||  |   | |||    | ||    | ||  | ||  | || || |||||          | ||||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| ||||| || ||||| || || |||||||| || || |  || |||||||
-taaattggagttgcttttaaaatggattcccttagttttctcggcagccaaacagagctggattgtgaatttataatcaatctgattttatgttttgtagGTTGCTGTGGCTCATACAATTGGGCATGTGGCTGCAACAGTGAGTATGTCCAAGGTTGCGGTGTCTTTTACTCACATAATCAAGAGTGGTGAGCCTGCAT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S143_174V6.1 (Physcomitrella patens), 3'ss of exon 1
----------gtgagttg-attattttgtgccagtaacttcttttattttatttacctgcctggaaaagtgtaactgaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
          ||| |  |  ||  || ||||  || |  ||    | |     |        ||     | ||||    |   |   |   |   ||||||| ||  ||||||| || ||||| || || || || || ||||| ||||| ||||| |||||||||||||||||||| || || ||||||||||| ||||
cggcaaacgtgtgtgcagtgttcgttggtgcttgtgagatcgagcactagcagttttattgggggctgttctaaccttttcatggtttgtgcaattgaagGTGGCATTGGCGCACACGATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCAGAACCCGCAT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S190_76V6.1 (Physcomitrella patens), 3'ss of exon 2
gtgagttgattattttgtgccagtaacttcttttattttatttacctgcctggaaaagtgtaactgaatttggtgattaact--------gatgaagGTTGCTG--------TGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
     |    |  | |||||   | |  | |  | ||      ||    |      | | | |  || | | ||  | ||||         ||| |  ||| |         ||||||| |||||||| || || || || || ||||| ||||| ||||| |||||||||||||||||||| || || ||||| ||||| ||||
-----tcagcttgtgtgtgcagttcaggtttggtgttcatgagactaagcactgggaatcttatcgagtattgttctgaacttctcacgaaatgtacattgttagGCGGCATTGGCGCACACAATTGGGCACGTGGCAGCGACTGTGAGTATGTCGAAGGTTGCAGTGTCATTCACACACATCATCAAGAGCGCGGAACCCGCAT

upper sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S241_24V6.1 (Physcomitrella patens), 3'ss of exon 1
------------gtgagttgattattttgtgccagt--aacttcttttattttatttacctgcctggaaaagtgta--actgaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
             ||  || |||||||| |     |  ||  | |     | | | ||   || |||   | ||||  |||||||     | |  ||| ||| |||| ||  | || ||||||||||| ||||| || || |||||||||||||| ||||| ||||| || ||||||||||| || |||||  | ||||||||||
caggaaaggtttctgttttaattattttttctagattaaaaatttggagatatgtctatgagcttggttgaatgtattactgaatc----ggtgcact-atgcagGTAGCGCTAGCACATACAATTGGTCATGTGGCAGCGACAGTGAGCATGTCGAAGGTTGCAGTATCTTTCACACACATCATCAAAAGTTCTGAACCTGCAT

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|67042737|gb|CO468992.1|CO468992
EST:     TTGTTGAGGCCCCTAAGACCGACCTGGACTTCTGGAAAGTTCTTTTCCCG                         GTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCT
genomic: TTGTTGAGGCCCCTAAGACCGACCTGGACTTCTGGAAAGTTCTTTTCCCGgtgagttgat ... actgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCT
EST: gi|211029602|gb|FL384590.1|FL384590
EST:     TTGTTGAGGCCCCTAAGACCGACCTGGACTTCTGGAAAGTTCTTTTCCCG                         GTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCT
genomic: TTGTTGAGGCCCCTAAGACCGACCTGGACTTCTGGAAAGTTCTTTTCCCGgtgagttgat ... actgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCT
EST: gi|67042492|gb|CO468747.1|CO468747
EST:     TTGTTGAGGCCCCTAAGACCGACCTGGACTTCTGGAAAGTTCTTTTCCCG                         GTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCT
genomic: TTGTTGAGGCCCCTAAGACCGACCTGGACTTCTGGAAAGTTCTTTTCCCGgtgagttgat ... actgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCT
EST: gi|6021272|gb|AW066200.1|AW066200
EST:     TTGTTGAGGCCCCTAAGACCGACCTGGACTTCTGGAAAGTTCTTTTCCCG                         GTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCT
genomic: TTGTTGAGGCCCCTAAGACCGACCTGGACTTCTGGAAAGTTCTTTTCCCGgtgagttgat ... actgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatttacctgcctggaaaagtgtaactgaatttggtgattaactgatgaagGTTGCTGTGGCGCATACAATTGGCCATGTTGCTGCTACAGTGAGCATGTCTAAGGTGGCAGTGTCATTCACACACATAATTAAAAGCGCAGAACCTGCAT
                              tgaattt  TA-rich tract