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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT

Basic information

species Zea mays
transcript AC216067.3_FGT002
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06890.1 (Oryza sativa), 3'ss of exon 2
taatctcc-tttctttgagcgtttcttcttttaagga---ggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
    |||  | |   |||       || | || ||     |    |||        |    | ||   |||  | |  || || |     |    || |  |||||| |||||||| || || |||||||| ||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| || || ||||| 
---cctcggtgttcatgactaccctttgtgttgagagcttgaggctactcctaagctgcctactttggattacaatt-ctgatatctcttgttggtgttggcagGGCAAATGCACAGCAACCAAAGCTTTTCGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCCCTGTATGGTCTCATTGTGGGCATCATCCTC

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G03470.1 (Glycine max), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatt-tcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
   ||  ||     |     ||  ||| |  |   | | | ||  |   |  ||   || ||||   ||    ||| | |     |    ||  || | || || ||||| || || |||||||| ||||| |||||||| || ||| | |||||||| ||||| ||||||||||| || |||||||| || || ||||| 
-tctcagctaaaactatagtttgtttcgtagatctatgtaatatgtatgttattattaactgaatacttgaacactgagtaaggtgattcctttttgttagAGCTAATGCCCAGCAACCGAAGCTGTTTGTTGGCATGATTCTTATCTTGATTTTCGCTGAAGCTCTTGCTCTGTATGGCCTCATTGTGGGTATCATCCTC

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA16G24220.1 (Glycine max), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttggga---attgaaattttattgacttattttctgggccactgattt-cagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
     | | || || |  |  | ||  |  | | ||        ||  | ||||  |    |||   |     |  |  |    |   ||  |||  ||| ||| || ||||| || ||||| ||||||||||| || ||||| |||||||||||||| || || ||| | ||  | ||||||||||||||||| || ||||| 
----atgcatttttagttcactcctgttgattatgaatttactaatagtaatttaagcttcattttgacgaattgaatatgacatgccggtaactcttttgcagAGCAAATGCTCAGCAGCCAAAGCTTTTTGTTGGAATGATACTCATCCTCATTTTTGCTGAGGCGTTGGCATTATACGGTCTCATTGTTGGCATCATCCTC

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G00980.1 (Glycine max), 3'ss of exon 2
---taatctcctttctttgagcgttt-cttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
   ||   |  |  ||||    | || | | | ||   | |    |    |   ||||     ||  |||  || ||| | | |   |   |  ||     ||| || ||||||||||| || || |||||||| || ||||| |||||||||||||| || ||||| ||||| || || |||||||||||||| |||||||| 
atatatctttttgcctttactagcttgcatttgttgttgtgaatttgacagtggattttccttttacaataatactgattaagtcaatctacttcta----cagAGCCAATGCACAACAACCAAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAAGCACTTGCCCTTTATGGTCTCATTGTTGGTATTATCCTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G23990.1 (Glycine max), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatt-tcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
|  | | ||    |  |   |   || ||| |  ||   | |  |   |||||    | |  | | ||    |     |    |    |  |  || ||||||| ||||| || ||||||||||| ||||| || ||||| || ||| | |||||||| ||||| ||||||||||| || |||||||| || || ||||| 
tgcttttctcagctaaattatagtttgtttcatagatcta-tgtaatgttattattaactgaatacttggacgctgagtaaggtaattccttttttgtcagGGCTAATGCCCAGCAGCCGAAGCTGTTTGTTGGTATGATTCTTATCTTGATTTTCGCTGAAGCTCTTGCTCTGTATGGCCTCATTGTGGGTATCATCCTC

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G00950.2 (Glycine max), 3'ss of exon 1
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttc---agGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
  | |   | |||||    |  | | ||   | | |     |      ||    | | |||    |||||      || |   |   | |     |||   || || |||||||| ||||| || |||||||| || ||||| |||||||||||||| || ||||| ||||| || || ||||| || ||||| |||||||| 
-gaacatatatctttt--tgcctttactagcatgcatttgttgtgaatttgacggtggattttccttttacaataatactgattaatcaatctgcttctgcagAGCCAATGCACAGCAGCCAAAACTTTTTGTTGGAATGATTCTCATCCTCATTTTTGCTGAAGCTCTTGCCCTTTATGGTCTAATCGTTGGTATTATCCTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G04090.1 (Glycine max), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgattt-------cagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
   | |   || |        ||       |    |  |  |  ||  | |||    ||| |||||||||    |||    | ||  | | | || |       ||| || |||||||| ||||| ||||||||||| || ||||| ||||| ||||| || || || || ||||| ||||| || ||||||||||| |||||||| 
---tgtatattttgctgatagtttgatacatggatataccttttataatgattcct-aatagaaattttac---cttgaagtttgaacaatttatcttcttatgcagAGCCAATGCACAGCAGCCAAAGCTTTTTGTTGGAATGATTCTCATTCTCATCTTTGCTGAGGCTCTTGCCCTGTATGGACTCATTGTTGGTATTATCCTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G11760.1 (Glycine max), 3'ss of exon 2
------taatctcctttctttgagcgtttcttcttt-taaggaggc-----agtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
      |  |    ||| |    |  | |  | ||| ||| ||        |  | || ||||||| | |   ||| ||| |   | |||| ||||             ||| || |||||||| ||||| ||||||||||| || ||||| || || |||||||| || ||||| |||||||| || |||||||||||||| |||||||| 
cattgatggttaattttatacagggatatagtttttataatgatattcctaataaaattcttattttgaa---gaagtttgaacaatttatcttctt---------ccgcagAGCCAATGCACAGCAGCCAAAGCTTTTTGTTGGAATGATTCTTATTCTCATTTTTGCTGAAGCTCTTGCTCTCTATGGTCTCATTGTTGGTATTATCCTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattt--tattgacttattttc-tgggcca---------ctgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
         |||| |  |    |    | | | ||| | | ||     | | ||| || |    ||    | ||   | |||||  |  || |          ||||  |||||| ||||| |||||||| |||||||| || || ||||| || |||||||||||||| ||||| |||||||| ||||||||||| || || || ||  | 
---------ttctctagg---atgaaatataatggaagaaatatcaattcaattgtgagtgtctatcccctgttatatcattttgatacgcaaatttgtggtttgatgacagGGCCAATGCTCAACAGCCAAAGCTTTTCGTTGGTATGATTCTTATCCTCATTTTCGCTGAAGCTCTTGCTCTATACGGTCTCATCGTCGGGATCATTTTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: AT1G75630.2 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------------------------------------taatctcctttctttgagcgtt-tcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
                                                                                              |  |      | |   || || | ||||||||      |  ||  ||      |   | |   || | | ||   ||| | ||   | |     || ||| |||||||| ||||| |||||||| |||||||| ||||| || || ||||| || || ||||||||||| ||||| |||||||||||||| || ||||| 
gtaacgttgtttgatattagatttggtgttggttaagaactgtctggattgaatctttgaagcagattaggataaattaccagtagaattcaacaggcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcat--cattcagaactctgttttgttaatctcaatgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: AT4G34720.1 (Arabidopsis thaliana), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaatttta----ttgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
        ||   |   |   | || ||  | |  | ||  |      ||||    ||  || ||  ||     ||||||||   | | |        ||||||||| ||||| || ||||| ||||| ||||| || ||||| || ||||| ||||||||||||||||||||||| ||||| || ||||| ||||| || |||
------gtttgtctctcgtcctcctgctactgat-acgctttgaggtattatggaagatatgtaacattggtgtttgacttacccttttgcgattctttttcagGGCAAATGCTCAGCAGCCTAAGCTCTTTGTTGGGATGATTCTTATCCTTATTTTCGCAGAAGCGCTTGCTCTTTACGGGCTTATTGTAGGAATCATTCTT

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: AT1G19910.1 (Arabidopsis thaliana), 3'ss of exon 2
-taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
 || || |   || |       || |   |||  | | | |   |  | ||     ||  ||     ||| |     |  | | ||      || || ||| |||||||||||||| || ||| | |||||||| ||||| || || ||||| || || ||||| ||||| |||||||||||||||||||| || ||||| 
atagtcgcagctcctgatattgttgtaagtttttgtatggaactcgagttttgaaaggtgttatgtgtttgtaattctggtgtgtgtttttgtg-ttgcagAGCGAATGCACAACAACCTAAGTTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCTGAAGCACTTGCCCTGTACGGTCTCATTGTTGGTATCATCCTC

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: AT1G75630.1 (Arabidopsis thaliana), 3'ss of exon 2
-taatctcctttctttgagcgtt-tcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
  |  |      | |   || || | ||||||||      |  ||  ||      |   | |   || | | ||   ||| | ||   | |     || ||| |||||||| ||||| |||||||| |||||||| ||||| || || ||||| || || ||||||||||| ||||| |||||||||||||| || ||||| 
acaggcgttgcacctgatgctttgttttcttttacatcaactatatgtgacagcat--cattcagaactctgttttgttaatctcaatgtcttattttgcagAGCGAATGCGCAACAACCGAAGCTGTTTGTGGGAATGATTCTGATTCTCATCTTTGCGGAAGCGCTTGCACTGTATGGTCTCATTGTTGGTATCATCCTC

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g13630.t01 (Vitis vinifera), 3'ss of exon 2
---taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaa-attttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
    |   |    | | ||    |  ||| ||  |   |  || | | |  ||||||       ||  || || ||| || | ||  ||    | |   | ||| || ||||| || ||||| |||||||| || || ||||||||||| ||||| || || ||||| ||||| ||||| || || |||||||| || ||||| 
tttcatattaggatttctgcctttgcctttttacatctattcaattc-tatttatttcctttaagagtatgtttttgtctgaattgttgttatatt---tgcagAGCCAATGCTCAGCAGCCAAAGCTTTTCGTTGGAATGATCCTCATTCTCATCTTTGCTGAAGCTCTTGCCCTGTATGGACTTATTGTTGGCATCATCCTA

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: Vv03s0038g00790.t01 (Vitis vinifera), 3'ss of exon 2
-----taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
     || | |       || ||  |   ||  |||  |  |     | || |||  || | |     |||  || |   | | | | ||      |  || |||||| ||||| || ||||| || |||||||| || ||||||||||| ||||| || || ||||| || || || ||||| || |||||||| |||||| | 
gactgtactttggacgactttaggataagttgctttg-gctgaggacaaattctttgttagtaggactaatcataat--ttgaatctatgatttgtt--ttgcagGGCTAATGCGCAGCAGCCTAAACTTTTTGTTGGTATGATCCTCATTCTCATCTTTGCTGAAGCACTGGCCCTATACGGCCTTATTGTTGGCATTATCTTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g02650.t01 (Vitis vinifera), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaag-gaggcagtacatgcttatttgggaat-tgaaattttattgacttattttctgggcc---actgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
      | | |||     |    ||  ||| ||  ||  ||  | || ||   |||    | |   || |  ||  ||| ||| |   |     | |  ||||||||| |||||||| ||||| ||||| |||||||| ||||| ||||||||||| || || |||||||||||||| || || || ||||| || || || |||
-----acttctctcccctcccccctcatttgaaatgaaacatcaaatcctccattgatggtgttgtatatgtttaccttttttcccctgttgggattattttcagGGCTAATGCACAGCAGCCAAAGCTGTTTGTGGGTATGATTCTCATCCTCATCTTTGCTGAAGCGCTTGCTCTTTATGGCCTGATTGTCGGCATCATTCTT

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: PP1S45_100V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgg----------gccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
                                                                                          |      |  |  |||  |        ||| |||| ||||     | |      ||  |||   | || | ||  |  ||  |            | ||  | || |||||||||||| || ||||||||||| || ||||| |||||||| |||||||||||||| || ||||||||  |||| || || || || || |||||| | 
gtagcggacgaacccttgcaatgtggtgatgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttatgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCATTTTCGCTGAGGCGCTTGCCTTGTATGGACTGATCGTCGGCATTATCTTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: PP1S45_97V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgg----------gccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
                                                                                          |      |  |  |||  |        ||| |||| ||||     | |      ||  |||   | || | ||  |  ||  |            | ||  | || |||||||||||| || ||||||||||| || ||||| |||||||| |||||||||||||| || ||||||||  |||| || || || || || |||||| | 
gtagcggacgaacccttgcaatgtggtgatgtatgggaatacgtagtgaagttggaaagagagatgtaatcgggattgaaatggattcgcagagggttcacggtgatggacatgaggtttgaggatgcagagtgagttgtgggagggtttggtgtgttgtggatgtggttgttaacgtggaggatggcatcgtttgcagGGCGAATGCTCAGCAGCCGAAGCTGTTCGTGGGGATGATCCTGATCCTCATTTTCGCTGAGGCGCTTGCCTTGTATGGACTGATCGTCGGCATTATCTTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------taatctcctttctttgagc---gttt----cttcttttaaggaggcagtacatgctt-----atttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
                                                                |  |||| |||||| ||      ||     ||   |||  |     |    |   ||     ||    | |  |   ||| |  |     |||  |       ||    ||| || ||||| || |||||||||||||| ||||| |||||| | || ||||||||||| || || |||||  | ||||| || ||||| || || ||  | 
gtaataattcaagatctgagcacatctataagaaatgtgtaacacataggttgaatggtgaatcttgtctcttttcttcgattcaaattcagagctgacttttggatcataacctaccattggtaaatacatgcacgggggtttgaccggagggtttatt---tttttgtgcgcagAGCCAATGCCCAGCAGCCGAAGCTTTTCGTGGGAATGATCTTGATTCTCATTTTCGCTGAGGCTCTTGCCTTATACGGGCTGATTGTGGGCATCATTTTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
                   ||   |||  |  |  |      |  |  || || |  |  |  |  || ||||  || ||||            || |||||||||||| || || || ||||||||||| || ||||||||||| ||||| || || || ||  | ||||| |||||||||||||| ||||| ||||| 
-------------------gtaagttcgatcgatcaaaagccatctttttcttcgatatctcca--ttgattggtttgtttttct---------ttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTCATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: EFJ37480 (Selaginella moellendorffii), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaa---attttattgacttattttctggg---ccactgatttca--gGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
         |  |||||   |  |    ||        ||  |  | | |  | |  | |  |     |||| ||  ||   |||||      |||  | |||||  |||| || || |||||||| ||||| || |||||||||||| | |||||||| ||||| || ||||| ||||| |||||  | || || || || || |||
--------atcatttgaagatcgcgagcttggtcctcacaagatttccctgctggaaactccactctgttttcttctctggctttctcactttccatcgttttcacagGGCCAACGCTCAACAGCCAAAGCTCTTCGTGGGCATGATCTTGATCCTCATCTTCGCCGAGGCGCTGGCTCTCTACGGATTGATCGTGGGGATCATTCTT

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: EFJ33972 (Selaginella moellendorffii), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaa---attttattgacttattttctggg---ccactgatttca--gGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
         |  |||||   |       ||        ||  |  | | |  | |  | |  |     |||| ||  ||   |||||      |||  | |||||  |||| || || |||||||| ||||| || |||||||||||| | |||||||| ||||| || ||||| ||||| |||||  | || || || || || |||
--------atcatttgaagatcgggagcttggtcctcacaagatttccctgctggaaactccactctgttttcttctctggctttctcactttccatcgttttcacagGGCCAACGCTCAACAGCCAAAGCTCTTCGTGGGCATGATCTTGATCCTCATCTTCGCCGAGGCGCTGGCTCTCTACGGATTGATCGTGGGGATCATTCTT

upper sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 2
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
                   ||   |||  |  |  |   |  |  |  || || |  |  |  |  || ||||  || ||||            || |||||||||||| || || || ||||||||||| || |||||||| || ||||| || || || ||  | ||||| |||||||||||||| ||||| ||||| 
-------------------gtaagttcgatcgatcaaaaaccatctttttcttcgatatctcca--ttgattggtttgtttttct---------ttgcagGGCGAATGCGCAGCAACCCAAGCTTTTTGTTGGAATGATCCTGATTCTCATCTTTGCCGAGGCTTTGGCTCTATACGGTCTCATTGTGGGAATCATCCTG

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|20301437|gb|BQ164380.1|BQ164380
EST:     GGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAG                         GGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCAT
genomic: GGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAGgtaaagctcc ... ctgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCAT
EST: gi|33102071|gb|CF062031.1|CF062031
EST:     GGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAG                         GGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCAT
genomic: GGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAGgtaaagctcc ... ctgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 705

TTTTTGATGGCTACGCTCACCTTTCGTCCGGGCTTGCCTGTGGCCTTGCTGGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAGgtaaagctcc ... ctgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1007

TTTTTGATGGCTACGCTCACCTTTCGTCCGGGCTTGCCTGTGGCCTTGCTGGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAGgtaaagctcc ... ctgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 572

TTTTTGATGGCTACGCTCACCTTTCGTCCGGGCTTGCCTGTGGCCTTGCTGGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAGgtaaagctcc ... ctgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1200

TTTTTGATGGCTACGCTCACCTTTCGTCCGGGCTTGCCTGTGGCCTTGCTGGGCTTGCAGCTGGCATGGCCATCGGCATTGTTGGTGATGCTGGAGTCAGgtaaagctcc ... ctgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT
            aattgaaattttattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctcctttctttgagcgtttcttcttttaaggaggcagtacatgcttatttgggaattgaaattttattgacttattttctgggccactgatttcagGGCGAATGCACAACAGCCGAAGCTTTTTGTGGGCATGATCCTCATCCTCATTTTCGCAGAAGCGCTTGCTCTGTACGGTCTCATTGTTGGAATTATCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - -tacatgc