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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacatattttctctacatcaccttgttgaattggtgggtcttgcttttgactgcaatacattaccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG

Basic information

species Zea mays
transcript GRMZM2G116840_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 5
gttacatattttctctacatcacct--tgttgaattggtgggtcttgcttttgactgcaatacattaccgat---------tgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG
|||| | |  ||| ||   ||  ||  |||| || |||  | || ||| | ||||   | || ||      |         |||||||||| || || || |||||||||||||||| |||||| |||||||||||||| ||||| ||||||||||||||||| ||||||||||  ||||||| ||
gttatagagcttcactgtgtcctctcctgtttaaatgg-agatcatgcatctgaccatattatatgtttattatatgttggtgcagCAACGTCCTGCCGACAATGATCGCTATGTCAGGAACTGCCGCAATGGGAGGTCGCCGAAGGAGACCAGGTGGTGGTTTCATGATGACAAAGTGTGATTGG

upper sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G37480.1 (Glycine max), 3'ss of exon 5
---------------gttacatattttctctacatcacc--ttgttgaattggtgggtcttgcttttgactg-caatacattacc-gatt------gcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG
                 |    | |||   ||  |||    |   | |     ||||| |   ||| |  |   ||  |||| |  ||||      |||||||||||| |  |||||||| |||||||| ||||||||  | ||||| || || || || ||||| ||||||||||||||||||||||  || | ||   
attatttaagattctactggtgaatttaggtaggtcattgatccatcatcaaatgggtgtcattttggcttaataactcatttcttgatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAA

upper sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G07810.1 (Glycine max), 3'ss of exon 5
-----------------------gttacatattttctctacatcaccttgttgaattggtgggtcttgcttttgactgcaatacattaccgatt--gcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG
                       | |  || |        ||||      |       ||   |   ||||   |   |  ||| |||    ||  |||||||||||| |  |||||||| |||||||| ||||||||  | ||||| || || || || ||||| ||||||||||||||||||||||  || | ||   
tggttattatttaagattcttcaggtgaatttaggtaggtcatcgatccatcatgggtgtcatttcggcttaataactctttactttatttctttggcagCAACGCCCTGAAGATAATGACCGCTATGTAAAGAACTGCAGAAATGGCAGATCACCCAAGGAGACAAGGTGGTGGTTCCATGATGACAAAGTATAATAAT

upper sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------gttacatattttctctacatcaccttgttgaattggtgggtcttgct-------tttgactgcaatacattaccgattgca------gCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG
                  | |||  || | |     ||||    |  || |  | |  | |||        | | |||       |||  ||||  ||      |||||||||  ||||||| ||||| ||||| ||||||||    || ||||||||||| |||||||| ||||||||||||||||| ||||  || | ||   
gtttctacatttgatctctcacactttgtattgttgtcacaaattcaaactttttgaccctgccacacaactcttactatgtcttattgtcgatgacaatatcagCAACGCCCGACTGATAACGATCGATATGTGAAGAACTGCAAGAACGGGAGGTCTCCTAAAGAGACAAGGTGGTGGTTCCATGACGACAAGGTTTAATGAT

upper sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------gttacatatttt-ctctacatcaccttgt-tgaattggtgggtcttgcttttgactgcaatacattaccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG
                                   |||||  |   | || |  || |    || ||||     |  | |   | |    |  | | |    |  ||||||||||||||| || ||||| ||||| ||||| |||||||||   |||||||||||||| || ||||| ||||||||||||||||| ||||  || ||||   
gttctttcttcttcttcgtgtttccctattgacaagttacccaaagtactgtgaattatgaggtctgaaactaagaatatcaatgtgttttttattccgc--cttattgcagCAACGCCCTGCGGATAACGATCGTTATGTGAAGAACTGTAAGAATGGGAGGTCTCCTAAGGAGACGAGGTGGTGGTTCCATGACGACAAGGTTTGATGCA

upper sequence: GRMZM2G116840_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------gttacatattttctctacatcaccttgttgaattg-gtgggtcttgcttttgactgcaatacattaccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG
                                                       ||     |||    |    || | | ||  | || | | |  || ||  ||| |    | ||||      ||||||||||||| || |||||||| |||||||| || || ||||| ||||| || ||||| || ||||| || ||||||||||||||||| |  |||| || | 
gtttggttcaaattgtcaaagttttaagttttttaaacccctcctttcttcttaattttgcttttatctttttccagcctattttagtgtgagagcattactcatgagtttttt-cattg-----tgcagCAACGCCCTGCAGATAATGACCGCTATGTGAAAAATTGTCGGAATGGCAGATCTCCCAAGGAGACTAGATGGTGGTTCCATGATGATAAAGTGTAATAGA

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|211201084|gb|FL470739.1|FL470739
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAG                         CAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGgttacatatt ... ccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGG
EST: gi|88749741|gb|DY533882.1|DY533882
EST:     GTTCTATCTGTATCAGCATATTATTTATGCTGTCCAGCTCGCCAGAAAAG                         CAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGgttacatatt ... ccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGG
EST: gi|89248057|gb|DY619843.1|DY619843
EST:     GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAG                         CAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGG
genomic: GTTCTATCTGTATCAGCATATTATCTATGCTGTCCAGCTCGCCAGAAAAGgttacatatt ... ccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccttgttgaattggtgggtcttgcttttgactgcaatacattaccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG
                          ttttgac  putative branch site (score: 3)
                                    aatacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacatattttctctacatcaccttgttgaattggtgggtcttgcttttgactgcaatacattaccgattgcagCAACGCCCAGCTGATAATGATCGCTATGTCAAGAACTGTCGCAATGGGAGGTCTCCGAAAGAGACCAGGTGGTGGTTCCATGATGACACCGTGTGATCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG