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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaatgtagcctctcgagaactgttattgcatggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG

Basic information

species Zea mays
transcript GRMZM5G825524_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 19
-----------cttaatgtagcctc-tcgagaactgttattgcatggaatcagtct-tctttggaccaagcgctagtctcttttgta-----aattacat--tgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
             |  |||  |||  | ||    |||| ||   |    ||  ||| ||| |    |       |||||||| | |      ||| ||||  ||||      || |||||||||||||||||||||| ||||| ||||| ||||||||||| |||||||| |||||||| ||||||||| |||| |||||||| || |||||||||||||
gtaacaattactatgctgtttccttattgaattatgtttttctcttctctctctctctctctctctctcaaatcagtctcttctatgcacataataacatcctgctgaataattgtgcagTACTCAGCAAAACTTCTAAAGAAACCTGACCAATGCCGAGCGGTTTATGCATGTTCACACCTTTTCTGGACTGACGACCAAGACGGAATAATGGATGGTG

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 20
---cttaatgtagcctctcgagaactg--ttattgca--tggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
    ||       ||  | || || ||  |  | |||  ||  || | |||  ||    | | |   |  |  |     |||   |   || | |   |||   ||||| |||||||| ||| | ||||| |||||||| ||||||||||||||||| || || ||||| || |||| |||||| |||||||| || |  |||||  
agttttctcaagaccattagacaaatggatggtggcaaatgttattaatctcttt----ctatgtattcatgccaagcctaa--catgatgatctatctttccacaGTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGA-

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 19
------cttaatgtagcctctcgagaactgttattgcatggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
      |       |   |    |    |  |     |||  || | |||  ||    | | |   |  |  |     |||   |   |||| |   |||   ||||| |||||||| ||| | ||||| |||||||| ||||||||||||||||| || || ||||| || |||| |||||| |||||||| || |  ||||| |
ttaagacccggaccattatacaaaaggattgtggcaaatgttattaatctcttt----ctatgtattcatgccaagcctaa--catgatgctctatcttttcacagTATTCAGCAAAGCTTTTGAAGAAACCTGATCAGTGCCGAGCAGTTTATGCATGCTCTCATCTCTTTTGGGTTGATGATCAAGATGGTATTAAAGATGGAG

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 18
cttaatgtagcctctcgagaactgttattgcatgg-aatcagtcttctttggaccaagcgctagtctcttttgtaaa--ttacattgctattgtttta----tgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
                |       | ||   |||  ||| |||||   ||     |  |  | ||||||  |  ||   | |||  |  |   || ||    |||||||  |||| |||||||| ||||| ||||||||||| ||||| |||||||| ||||| ||| | ||||||   || || |  ||    |||   ||||| |
----------------gtatttcatcatgatatgataattagtct--cttaccatattcaattgtctctgcttaaaggctgacaagggaaaacttatactcttgcagTATGCAGCGAAACTTCTAAAGAAACCTGATCAATGTCGAGCTGTTTATGCCTGTTCTCATTTGTTCTGGCTGGAAGATCGTGAGACCATACAAGATGGAG

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
lower sequence: AT1G75850.1 (Arabidopsis thaliana), 3'ss of exon 19
cttaatgtagcctctcgagaactgttattgcatggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
                 | || | || |  ||  || |     || |     |      ||    |  | |  |||      |  | |  || |   |||||||||||||  ||||| ||||||||||| ||||||||||| ||||| || || || || || || ||||  ||||| | |||||| || |  ||||| |
---------------gtacaaatattttgccaatgatttctcattttacaagctttcttctcaatttctatccaaacgcttatattttctttgtgaccagTACTCAGCAAGGCTTCTTAAGAAGCCTGACCAATGCCGAGCGGTTTACGCATGCTCTCACCTCTTTTGGGTCGATGATCCAGATGGTATTAAAGATGGAG

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 19
cttaatgtagcctctcgagaactg--ttattgcatggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
      |||   |    |||| ||  |   |  ||  || ||||      ||   |    |  |  ||  |||| |         ||| || ||||  |||||| || ||||| ||  | |||||||||||||| ||| |||| |||||||| || |||||||| ||||||| ||| || |||||| | || |  ||||| |
------gtaatattagtagaattgcatctctttataaaaccagttcagcctgtctctgctgaaaccctgatttgaa---------gcttttattttgagcagTATTCTGCAAAGCTGTTAAAGAAGCCTGATCAGTGCAGAGCCGTTTATGCATGCTCACATCTCTTCTGGGTTGACGATCAAGATAGCATCAGAGATGGAG

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 19
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 19
--cttaatgtagcctctcgagaactgttattgcatggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
    ||||||   |  || |    | | |||   | || |   |   ||||  |     |   |||   ||       || | ||  | ||   ||   ||||| |||||||| ||| | ||||| |||||||||||| ||||||||||||| ||||| |||||||| |||| ||| || |||||||| || | |||||| |
gtagtaatgtttacattcta----tctgattattttgacttgttgaactttctat--gccaaaagttgtttaaaccttttccttttgtctttccttggccagTATTCAGCAAAGCTTTTAAAGAAACCTGATCAATGCAGAGCAGTTTATGCATGTTCCCATCTTTTTTGGGTTGACGATCAAGATGGCATTAAGGATGGAG

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|14203142|gb|BG836819.1|BG836819
EST:     ATATATTTGGGGTGGAAAATAGAGACACACTCACTCACAAGACAACAGGG                         TACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCG
genomic: ATATATTTGGGGTGGAAAATAGAGACACTCTCACTCACAAGACAACAGGGgtaatggttc ... ttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG
                                          ttgtttt  CT-rich tract
                      ttttgtaaattacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaatgtagcctctcgagaactgttattgcatggaatcagtcttctttggaccaagcgctagtctcttttgtaaattacattgctattgttttatgcagTACTCAGCAAAACTTCTCAAGAAGCCTGATCAATGCCGAGCAGTTTATGCGTGTTCACATCTTTTCTGGGCTGATGACCAAGATGGGATAATGGATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG