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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttttcatacttgtgtacattgacctgttctttgaacaatatgtacatcagttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT

Basic information

species Zea mays
transcript GRMZM2G161418_T06
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
gtaactttttcatacttgtgt-acattgacctgttctt-tgaacaatatgtacatc----agttgc-----------taagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
|||||| |||||  ||||  | |  || | |||| | | ||   |  |  |||||     | |||            ||| |   ||  |||  ||||||||| ||||||||||| |||||||||||||||||||| || |||||||| ||||| ||||| |||||||||||||||||||| |||||||||
gtaactatttcaagcttgcttgattttcatctgtgcatgtgcctaccaaatacattctgtaattgtacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
---------------gtaactttttcatacttgtgtacat---tgacctgttctttgaacaatat-gtacatcagttgctaagttgct-gttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
                | | |  ||   |  |||| | ||   |  | | ||| ||    || || |||| | | |   ||| |   | |  |||  |||||| || ||||||||||| |||||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||||||||| |||||||||
gtaactatttcaggcttgattaattttcatctgtgcaaatgcctaccattttcattctgtaagattgtacctaaatgtttaactcatttgcactataccagGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
--------gtaactttttcatactt-gtgtacattgacctgttct---ttgaacaatatgtacatcagttgctaagttgct--------gttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
         |  || ||||  | |   |||   |||  || ||||   |  ||| || |     |   || |||| | | |         || |   | ||||||| || |||||||| ||||| |||||||||||||||||||| || ||  |||| ||||| ||||||||||| |||||||| |||||||||
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
--------gtaactttttcatac-ttgtgtacattgacctgttctttg----aacaatatgtac------atcagttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
          ||| | | || |  || | |   |||   |   || |     | || | |||        ||   || ||   |   | ||||     ||||||||||||||||||| |||||||||||||||||||||||||| || ||| | |||||||| ||||| ||||| |||||||| |||||||||
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 6
-----gtaact-ttttcatacttgtgtacattgacctgttctttgaacaa------tatgtacatcagttg----ctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
       | ||  | | | | || | |   |||   |   || |  | ||      | ||  |||   ||     ||   |   | ||||     ||||||||||||||||||| |||||||||||||||||||||||||| || ||| | |||||||| ||||| ||||| ||| |||| |||||||||
gtacaacatctactctgaaaattttatcagttgttttccactctacagaagtagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
-----------------gtaactttttcatacttgtgtacatt---gacctgttctttgaacaat-atgtacatcagttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
                 | || || |   |  || |  ||  |   ||  |  | | ||| || | |  ||   |  ||  |   ||  ||| ||     |||||||||||||||||||||||||||||||||||||||| ||||| || ||| | || ||||| ||||| ||||| |||||||| |||||||| 
ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtgatcattgacttattccttttttttcttttttgtgct---ttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------------gtaactttttcatacttg-tgtacattgacc-tgttctttgaacaatatgtacat------cagttgctaagttgctgttc------taagcc--agGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
                                                                    | |||  |  | ||  |  |  |||  | |  | ||   || |||  ||  |         || |||| | | | ||       || ||   ||||||| || |||||||| ||||| |||||||||||||||||||| || ||  |||| ||||| ||||||||||| |||||||| |||||||||
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
----------gtaactttttcatacttgtgtacattgacctgttctttg-aacaatatgtacatcagttgctaagttgct------gttctaagcc--agGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
          | |||| ||| || | ||| | |  |    |  ||  || ||| || |     |   || |||| | | |      ||  || ||   ||||||| || |||||||  ||||| |||||||||||||||||||| || || | ||| ||||| ||||||||||| |||||||| |||||||||
aatctttgctggaactgtttaatccatgtttgctgttcttttctcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
--gtaactttttcatac-ttgtgtacattgacctgttctttg----aacaatatgtac------atcagttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
    ||| | | || |  || | |   |||   |   || |     | || | |||        ||   || ||   |   | ||||     ||||||||||||||||||| |||||||||||||||||||||||||| || ||| | |||||||| ||||| ||||| |||||||| |||||||||
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtaactttttcatacttgtgtacattg----acctgttctttgaacaatatgtacatcagttgc--taagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
    || || || | || | |   |  |     |  | || | | |    |   || |  |  |    | | ||| |       || ||||||| ||||||||||||||||| || |||||||||||||| || || || || ||||| || ||||| || ||||| | ||| |||||||||
gtacaatttctttaaaccttttccctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc-agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------gtaactttttcatacttgtgtacattgacctgttctttgaacaatatgtaca--tcagttgctaagttgctgttctaagc---cagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
                                                           | | |     || | ||||||  || | | |       ||  |  | || |    |||    || |||||| |   |     |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||||||||| || |||||||| |||||| |||| |||||||||
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------gtaact--ttttcatacttgtgtacattgacctgttctttgaacaatatgtacatcagttgctaagttgctgttct---------aagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
                                   ||| |   |||   |  |  | | | |   | |||| |||   || | |    ||    |  | |  ||||||| |          |   ||||||||||||||||||| || |||||||| |||||||| || || || || |||||||| |||||||||||||||||||||||||| || || 
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattga-ctgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------------------------gtaactttttcatacttg-tgtacattgacctgttctttga-acaatatgtacatc--------agttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
                                                                               |||  |  ||   | | | |  |  ||  |||     |||  ||  | || |  |         |  ||  | |    | |  |    ||||||||||| ||||||||||||||||| || ||||| ||||| || || ||  | || || ||  | || ||  |||| |||  ||| ||||||
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcctagctattgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT

upper sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5
gtaactttttcatacttgtgtacattgacctgttctttgaacaatatgtacatcagttgctaagttgctgttctaagc-cagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
                   |||    |||     |         | ||  | |||    || |||  |     | | | |||||||||||||| ||||| ||||||||||| ||||| || ||||| || || ||  | |||||||| || ||  |||| |||  ||||||||| 
-------------------gtatgaagacgaaaacacattgtggtctgagc-tcaa--acttagtaacgtccgtgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

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|32914682|gb|CF019494.1|CF019494
EST:     GCCCGCATTATTCAGAAACTTGGTTTTCCAGCTAAGTTTAAG                         GATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATT
genomic: GCCCGCATTATTCAGAAACTTGGTTTTCCAGCTAAGTTTAAGgtaacttttt ... tctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctgttctttgaacaatatgtacatcagttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
 cattgac  putative branch site (score: 3)
                                         ctgttct  putative PPT
             aacaatat  TA-rich tract