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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatcctttctgttcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT

Basic information

species Zea mays
transcript GRMZM2G443953_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 11
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggat-atttaaaaaacagtaactaatcctttctgttcttc------cagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
       | |  ||    ||   |   ||  ||  |  |   |||| |   |  || |   |  ||| |      ||  || ||  ||  | |  ||       |||| ||||  |||||||||||||||||||||||||| ||||||||||||||| ||||||||||| ||||| ||  | |||||||||||||| || ||||| |
-----agaagtgagttttaaaataatagtcctt--attgcgggttcaattatcagcaatatttgttttatgggtggtggctgattgttgatttcatttattgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTATGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 11
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggat-atttaaaaaacagtaactaatcctt--tctgttct----tccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
       | |  ||    ||  ||   ||  ||  |  | | |||| |   |   | |   |  ||| |      || ||| ||  ||  | |  | |    | |||| ||||  |||||||||||||||||||||||||| ||| ||||||||||| ||||||||||| ||||| ||  | |||||||||||||| || ||||| |
-----agaagtgagttttaaaacaatagtcctt--attgctggttcaattatcaacaatatttgtttcatgggtggtgacttattgttgatttaatttgttgtgcagAATTTAAAGCACAATCCAAATGGGAGGTTTGTTGTTGTGTGTGGAGATGGTGAGTACATTATATACACTGCATTGGCATGGAGAAATAGGTCATTTGGTT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 11
tttttttatggaaggaaaaaggcaccggtt--ttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatcctt--tctgttctt-----ccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
           ||  || ||  ||||  ||  ||||||   | |   || | ||||  |   ||   |    |   ||  || |    |  | |  | ||     | |||||||| |||||||||| |||||||||||||||| ||| ||||||||||| ||||| ||||| ||||| |   | ||||||||||||||||| ||||| |
---------taaaataataatccaccccttagttttaattatcaccacttatttattttttcatgcatgttgactggtgtctgacttgtgatttacttttatactcaagAGTTTAAGGCACAATCCGAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGGGAGTATATTATATACACTGGTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 11
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatccttt-ctgttcttc-cagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
    ||||   |    ||   || ||    ||||||   ||    ||   || |   || || || |        | |||  |  ||| || || ||| |||||| || |||||||||||||||||||||| |||| ||| ||||||||||| || || ||||| ||||| ||  | ||||||||||||||||| ||||| |
-agcttta-aaataataatctgccccttagttttaattatttccacttttttttttaagcatgttgactggtgtctgacttgtgatttacttttattctcagAGTCTAAGGCACAATCCAAATGGGAGGTTCGTTGTTGTTTGTGGAGATGGGGAATATATTATATACACTGCTTTGGCATGGAGAAATAGATCATTTGGTT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 11
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaa--acagtaactaatcctttctgttcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
 |  |  |||  |  ||  |  |  | ||||  ||  |  |      |   |   | || ||| |||       |   |  ||   || |     ||  ||||| ||   |||||| || |||||||||||||| |  || || || |||||||||||||| |||||||| ||  | || |||||||||||||| |||||||
-taatagatgataaaaatgaaac-tctgtttcatatgaagtcccaagagtgtggtccagaataattatgtcttgcctcacatatagctattctaactctcagAGCTTGAAGCACAACCCTAATGGGAGGTTTGTCGTAGTCTGCGGTGATGGAGAGTACATAATCTACACTGCTTTGGCGTGGAGAAATAGATCTTTTGGGT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 11
---tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatcctttctgttcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
   ||    || ||| | |  |  |   |     | |   | ||  || | | ||||| |   | |||||        |   |  |  ||| |  | || |||||  ||   || || ||||||||||||||||||| ||| ||||||||||| ||||||||||| || |||||  | |||||||| ||||| || ||||| |
gcattaagcta-ggatgaatgattgtttccaccatattttaatttattgttatttatgtt--tacatttatttcttccttttttttttttttttgtgtttcagAGCCTAAAACATAACCCAAATGGGAGGTTTGTTGTTGTTTGTGGAGATGGTGAGTACATTATATATACAGCTTTGGCATGGAGGAATAGGTCTTTTGGTT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 11
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatcctttctgttct---tccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
  ||||| |  |||    |  |||  |  | | |    | |   | |   || || |   | |||      |  |    |  |  |||  ||| |   | ||||||||   ||||||| | ||||| |||| ||||| ||| ||||| ||||| || ||||| || |||||| |  | ||||||||||||||||| ||||| |
actttttctctaagaggcagtgcatagaatatgtgcgggctcagttt---ttttgttgtcacattatggttaatgacttttgtttttttggttttaatttcagAGTTTGAAGCACAATTCTAATGGAAGGTCTGTTGTTGTTTGTGGGGATGGGGAATACATAATATACACATCTTTGGCATGGAGAAATAGATCATTTGGCT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 12
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 11
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttct---aacttatgct-----aggatatttaaaaaacagtaactaatc------ctttctgt-tcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
     | |  ||  |        |     ||||| ||| ||  |  |   ||  |||| |     |  |||| ||  ||       || |||      |||| |||  ||| |||||  |    || ||||| ||||| |||||||| |  || ||||| ||||| ||||| |||||||||||||| || || ||||| ||| |||| ||||| |
----gtgaccgattgctcgtctaaatttctttttgaaatttcatcttcgaaagatatgtttgctcaaaatatctatcaagtgaacgcttatcggttggctttgtgtgccttgcagAGCCTGAAACATAATCCGAATGGCAGGTTTGTGGTAGTTTGTGGTGATGGTGAGTATATTATCTACACAGCTCTTGCTTGGAGGAATCGATCATTTGGTT

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|160481610|gb|EY254442.1|EY254442
EST:     GTCTGCCATTGGCTGTGAAGGAGCTAGGAAGTTGCGACCTTTACCCACAA                         AGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGA
genomic: GTCTGCCATTGGCTGTGAAGGAGCTAGGAAGTTGCGACCTTTACCCACAAgtaggtttat ... gttcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacttatgctaggatatttaaaaaacagtaactaatcctttctgttcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT
                                     tcctttctgttcttcc  CT-rich tract
               atatttaaaaaacagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttttatggaaggaaaaaggcaccggttttttaaaagttagttctaacttatgctaggatatttaaaaaacagtaactaatcctttctgttcttccagAGTTTACGGCACAATCCAAATGGGAGGTTTGTTGCTGTATGTGGAGATGGAGAGTACATTATCTACACAGCGCTAGCATGGAGAAATAGATCCTTTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA