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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtcattatttgtttccttatttgaattgttcattatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG

Basic information

species Zea mays
transcript AC209208.3_FGT001
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g44642.1 (Oryza sativa), 3'ss of exon 3
ataactctaaactatcatctg--tcttgactagctaaatgttttattgcacttggtcattatttgtttcctt----atttga------attgttcattatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
            |||| | ||  |  ||     || | | |||||||     || ||||  ||||||||  |    ||||||      ||  |||  | |||| | | ||||||| | ||||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||| | || |||
------------tatcctttgagtagtgtgccactgactattttattaggactgatcatcctttgtttctcttcaaatttgatataatataattctctgtcatttgtatcagTGATAAAGGTGAAATGTGTGCAATGAAGGAGGTCACCCTTTTCTCAGACGATCCTAAATCAAAAGAAAGTGCAAAGCAGTTGTGTCAG

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 4
--------ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtcattatttgtttccttatttgaattgttc--------attatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
         | | |  |||   || |   |  | | |   |   | ||||| |  |     ||   || ||  || | ||  |||||| |         ||  |  ||| ||| ||||| ||||| |||||||||||  |||||||||||||||| || ||||||||||| || || |  |||||||| || ||  |    |||
gtatgcattttagttaaaatgttcttaatttctcatttattcctttttttaatctatcatttctacatatggatcttaataagaattgctttgtttaaaatgtttgtctcttttagTGAAAGAGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCGAAGCAATTTATGCAG

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 2
ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtca----ttatttgtttccttatt-tgaatt-gttca--ttatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
     |  |  ||    | ||| | || || ||  ||||||| ||   ||   |||     | ||   ||| | ||| ||| || |||||  || | ||    |  || ||  | ||||| |||||||| ||||||||||| |||||||| || |||||| |||||||||  ||||||||  | || ||  |||| 
-----ttcatgctt---tgtgtgtggattatctttatgttttttttttctgcatcaagtccttttaacttcttaattgtgacttagttcaacttctgatgatctatagAGAATGTGGTGAGATGTGTGCAATGAAGGAGGTAACCCTTTTTTCTGATGATGCTAAATCAAGGGAAAGTGCGCAGCAACTTGGCCAA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 2
----------ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtc-attatttgtttccttatttgaattgttc------attatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
           | ||   ||  | |    | | ||    ||  |  | ||||||     |   || |||| ||  | | |  | | |||||||       | | |  ||   |  || || || |||||||||||||| ||||| ||||| || || || ||||||||| | ||||| ||||||||||| || ||  |    |||
gtatgtgcttgtgaccaaaagttcttgattatattatgaagaaatcttttttatacttttaaatccattagtttatacatcttataaattgtttggttaaaatgttgtcctgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTGTTTTCAGATGATGCCAAATCTAAAGAAAGTGCTAAGCAATTAATGCAG

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 2
ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtcattattt-gtttccttatttgaatt--gttca--ttatcatctatttca--gTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
       |   || || | ||| |   | || |    | | | |  || |||  |||||  | ||||| |  |||  ||    || |  ||| | |||  | ||  |||| || ||||| |||||||| ||||||||||| || ||||| ||||||||| |||||||||  ||||||||  |||| ||  |||| 
------ttgttctgtcgtttgtgtct-caaggtgtgggctatctatcatttgtgcattaaatagtttcttcttttacatctgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 4
--ataactctaaactatcatctgtcttgactagctaaatgtt--ttattgcacttggtcatt-----atttgtttccttatttgaattgttc--------attatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
  ||   | | |  ||  || | |||| | |    |  | ||  || ||  | ||  |||||     || ||  || | ||| |||||| |         ||  |  ||| ||| ||||| || || |||||||||||  |||||||||||||||| || ||||||||||| || || |  |||||||| || ||  |    |||
gtatgtattttagttaaaatgt-tcttaatttcacatttattccttcttttaatttatcatttctatatatggatcttaattagaattgctttgtttaaaatgtttgtctcttttagTGAAAGTGGCGAAATGTGTGCAGTGAAGGAGGTTACCCTGTTTTCAGATGATCCCAAGTCTATGGAAAGTGCTAAGCAATTTATGCAG

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 3
----------ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttgg--tcattatttgtttccttatttgaattgttc------attatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
           | ||   ||  | |    | | || |  |   ||   ||||  | |  ||     ||||| |   | | |  | | |||||||       | | |  |    |  || || || |||||||||||||| ||||| ||||| || ||||| ||||||||| | ||||| ||||| ||||| || ||  |    |||
gtatgtgcttttgaccagaagttcttgattatatt-atgaagaaatcttttttctacttttaaatccattagtgtatgcatcttataaattgtttggttaaaatgttgttatgtgtagGGAAAGTGGTGAAATGTGTGCTATGAAAGAGGTAACTCTTTTTTCAGATGATGCCAAATCTAAAGAGAGTGCTAAGCAATTAATGCAG

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 5
ataactctaaactatcatctgtcttgactagctaaatgtt-ttattgcacttggtcattatttgtttccttatttgaattg-ttca--ttatcatctatttca--gTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
    || |    | |  |||       |  | ||  | |  ||  |||| |   |  || |||  ||    || ||| ||| || |  ||| | |||  | ||  |||| || ||||| |||||||| ||||||||||| || ||||| ||||||||| |||||||||  ||||||||  |||| ||  |||| 
----ctgttg-tttttgtctcaaggtgcgggttatctatcattcgtgcattaaatagtt-tttacttttacatctgatttgatttagtttaacttctgatccatagTGAAAGTGGTGAGATGTGTGCAATGAAGGAGGTAACTCTTTTTTCAGATGATGCTAAATCAAGGGAAAGTGCTCAACAACTTGGCCAA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 2
ataactctaaactatcatctgtcttgactagctaaatgttttattgcact-tggtcattatttgtt-tccttatttgaattgttcattatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
||||  || |  | |  |||      | ||   ||  |    | |  | | |  |  || | |||   || | |||  || | | ||  |  |||   ||||||| || || || |||||||| ||||| |||||||| || | ||||||||||||||| ||||  || |||||| ||||  |  | || 
ataaa-ctgatttgttctcttcacaaaatattgaataggagaactcaaatgttatatttctatgtcacccctgttttgatcggttat-gttttcttcctcagTGAAAGTGGGGAGATGTGTGCCATGAAAGAGGTTACTCTATGCTCAGATGATCCTAAGTCAAGGGAGAGTGCACAACAATTGGGGCAA

upper sequence: AC209208.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 2
ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtcattatttgtttcct---tatttgaattgttcattatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
 | |   ||    | ||  ||  |||     ||  |||||||       |      ||| | | ||  |   ||| ||| || |  ||| |   ||  || ||||| || |||||||||||||| ||||||||||| || || || ||||||||| | || ||||| ||||||||||||||| |  | || 
cttatgatatctaagcaattgatttg--cgactccatgtttttaaatgttgatcttttactggatttgtgcatatctgattt-tatattttgtactggtttagTGAAAGTGGTGAAATGTGTGCAATGAAGGAGGTGACACTATTTTCAGATGATGCAAAGTCAAAGGAAAGTGCAAAACAGTTGGGGCAA

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|32837658|gb|CD977336.1|CD977336
EST:     AAATTGATTGGCCGTGGGACATTTGGCCATGTATATGTTGGTTTTAACAG                         TGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGA
genomic: AAATTGATTGGCCGTGGGACATTTGGCCATGTATATGCTGGTTTTAACAGgtatgccttt ... tctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGA
EST: gi|32838212|gb|CD977890.1|CD977890
EST:     AAATTGATTGGCCGTGGGACATTTGGCCATGTATATGTTGGTTTTAACAG                         TGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGA
genomic: AAATTGATTGGCCGTGGGACATTTGGCCATGTATATGCTGGTTTTAACAGgtatgccttt ... tctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGA
EST: gi|91877716|gb|EB407673.1|EB407673
EST:     AAATTGATTGGCCGTGGGACATTTGGCCATGTATATGCTGGTTTTAACAG                         TGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGA
genomic: AAATTGATTGGCCGTGGGACATTTGGCCATGTATATGCTGGTTTTAACAGgtatgccttt ... tctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacttggtcattatttgtttccttatttgaattgttcattatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG
                                             tctatttc  CT-rich tract
                       ttatttgaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataactctaaactatcatctgtcttgactagctaaatgttttattgcacttggtcattatttgtttccttatttgaattgttcattatcatctatttcagTGACAGAGGTGAAATGTGTGCGATGAAGGAGGTTACCCTTTTCTCAGATGATCCTAAATCAAAAGAAAGTGCAAAACAGCTCTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - tgcactt