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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT

Basic information

species Zea mays
transcript GRMZM2G149481_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
--------gtacgcaagcgtagc--gttgaagcataatatgcattc--tgtgggcctgtggcctgtggcctgtgggtgaccggc----cgagacgatgtgt-------gtgcttctgctgctc-tacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
          ||  ||||       |||       |  |||| | |  |    | |||      | |||   ||  ||| |       |    || ||||           ||| || |  |  ||    |  ||||| ||||| ||||||||||| || || || |||||||| ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||  
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
-------------------gtacgcaagcgtagcgttgaagcataatatgcatt-ctgtgggcctgtggcctgtggcctgtgg--gtgaccggccgagacgatgtg-tgtgcttctgctgctctacttgt-tgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
                     ||  |  ||||    |  |  || ||    ||| |||     |  |      |    ||     || |       ||  |   || | ||||| | |   | |  || |    || | || || || ||||| || || ||||||||  |||| || || || || ||||||||||||||||||||||| ||||| || || |||||||| ||  
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA06G11540.1 (Glycine max), 3'ss of exon 5
---------------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctg-tgggtg--accggccgagacgatgtgtgtgcttc---tgctgctctacttgttgc-----agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
                             ||   ||| ||   || ||||| |  |   |          ||    | ||||   |  |  ||   |  |      |  || ||||| ||||   |  |  |||   |||| |     ||||||| || |||| |||| | |||||  ||||  |||| ||||||||||| ||||| || ||||||||||| ||||| || ||||| |||||||| ||  
gtaaaaagactcgatatttaggagcctcaacatcagcataaaattaaagcaaatcaaataacaatgattgctaacacatgtgatataataagtattattgttgctaattatttgtgttcttcaattaatattctgtgtgtttctctaaagGTTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCGACCAACATTCTCTATACTTTTGGTGGGCATGCTGTTACAGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
---------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgt-gtgtgcttctgctgctctacttgttgc-------agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
                ||    |   ||    | |   || ||    ||| | |    |  |    | |      |  |  || | |    |    || ||     | || |  || | |||||         || | || || || ||||| || || ||||||||  |||| || || || || ||||||||||||||||||||||| ||||| || || |||||||| ||  
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA04G43150.2 (Glycine max), 3'ss of exon 5
---------------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtg-tgcttctgctgctctacttgttgc-----agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
                              |   | | ||   || ||||| |  ||  | |   ||   ||    | ||||   |  |  | |  |      |   |||||  | |   |  |  |||   |||| |     ||| ||| || |||| |||| | |||||  ||||  |||| ||||||||||| ||||| || ||||||||||| ||||| || || || |||||||| ||  
gtaaaaagactcgatatttaggagcctcagcatcatcataaaattaaagcaaatcatataatgattg---ctaacacatgtgatataagtattattgttgccaattttgtgttcttcaattaatattctgtgtgtttctctgaagGCTGAGGGGGTGACGCACACAGGGCCAGCCAAATTGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTATACTTTTGGTGGACATGCTGTTACAGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtg-tgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
           ||  |   ||   | |||| |    ||| |   ||| |    | |  | |   |           |  ||||  ||| |   || ||   || |      |||| || || |||||||| || || || | |||| ||||  | |||||||| ||||||||||||||||| ||||| ||||| || || |||||||| ||  
----------ttaatgcataaatgttatatac---ttgtagagttgtagataattgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT1G77690.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatg--tgtgtgcttctgctgctctacttgttgca--gGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
              | ||  |   ||| |   ||  |||     ||     | |    | | |       | |  |   ||   ||| |  |     |  | | | | |   |  || ||| |  ||||| ||||| || || ||||  |||||||| ||||||||||| ||||| |||||||||||||| || || || ||||| || || ||  
------------gtcattataat-taacacaaatcttgt---tttgattattataagatatagacatatagtcctggttattgttgtttaatatatttatttttcatataaaaaagGCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgtt-----gcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
          |||   |  |   ||   || ||  |       |     | | ||   |     | |      ||    || | | |  |  |  |  | || |||||     |||| | || || ||||| ||||| || ||  ||||| ||||||| |||||||| ||||| ||||||||||||||||| ||||| || || ||||| || ||  
----------gtactatacatatatctcattcaa-ccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatt--tatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgtt-gcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
                       |||  ||  |     |||  |   | | ||   | |  |   ||  |  ||     ||| ||    |  |    |     |  ||   |   ||||| | | |||||| | ||||||| || ||||||||||| || || ||||| ||||| ||||||||||| ||||| || |||||||||||||| || || || || ||||| || ||  
gtatgtatttaccttaattagctgtattcat-cacttagttttaatttcaaataattcccataatcccatcccc-----cctttgatacattgatttatttattaagtaatcccatgctgatttgcttgtttgaagGTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGT--

upper sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 4
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
    |  || | || |  |  |   | |||   ||  ||| ||       ||||  |      | ||   ||     |||| | ||    |||  ||     | ||    |||  ||    || |||||| | ||  ||| |||  |||||||||||||||| || ||||||||||| ||||| || || ||||| || || || || ||  
--gtgtgagtggagggaggggggcgagtata-gtttcgtgagct------ctgtcactatcacgaga---gctctttcgatctttgctaatctcttggaactcctgccatagGCGGACAATGTCAAGCACACTGGAGCGAGCAAACTGGTGCTCTACTTCACTGGAGCCACAAACATACTCTATACATTTGGAGGCCATGCGGTGACTGT--

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|91878597|gb|EB408554.1|EB408554
EST:     CTCGCCGTCGCGTCCCTCATCCATGGGCAG                         GTTGAGGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|148973556|gb|EE024660.2|EE024660
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCA
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCA
EST: gi|78125529|gb|DV543913.1|DV543913
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|148973555|gb|EE024659.2|EE024659
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|76285595|gb|DV025163.1|DV025163
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|94475284|gb|EB704242.1|EB704242
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|78120761|gb|DV539145.1|DV539145
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTAC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTAC
EST: gi|50327062|gb|CO522188.1|CO522188
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|76285596|gb|DV025164.1|DV025164
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|78120760|gb|DV539144.1|DV539144
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|86466052|gb|DY232425.1|DY232425
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
EST: gi|86466051|gb|DY232424.1|DY232424
EST:     CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAG                         GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC
genomic: CCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtacgcaagc ... cttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
                                        ctctactt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT