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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG

Basic information

species Zea mays
transcript GRMZM5G893864_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgt-tgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
             ||||       ||| ||| |||||   |  |||    ||||  |||   || ||||    || |  || | | |  ||||||||||| ||||||||||| || ||||||||||||||||||||||||||||| ||||||||||| ||||||||||| |||||| | |||||||| |||||||
------------gttagggaagttggagcttaataat---cttacacaattaatttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 27
--gtttggcctatttttagaatctaagg---atcttgataatacgcgcacatgcctaata--caacg--ttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
   |||||| |  | || || |   ||    || |   | ||     ||||   | |  |  || |   || ||| | ||||    |    ||| | |   |||| ||||||||||| || ||||| ||||||||||| || || ||||||||||||||||| || || ||||| || |||||||| || |||||||| || |
gattttggcttcatcttggattaagagataaatttatttcatggagacacaacacgagcattcagcagattatctgagatgtgtagttcactttgtgt---agGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAGCTCACTGTTAATGTAGCTGCTCTTGTAATAAATGTTGTGGCCG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 26
-------gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaataca-acgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
        | | |||     |   | | || | |   ||||  ||||     |||  | |  |  | || ||  | | | |   ||   |||   | |  |||| ||    ||||| || ||||| ||||||||||| || || ||||| ||||| |||||||| || ||| | ||||| ||||  || |||||||||||||
gtgtatcctatagcccgagatattattttatgtaagctgat--tacgaattgatgtttgaagcgtaagtggtactgcctttcaatttcttttgccaattcagGTTGTCAAATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTCAATATAGCAGCACTTGCTATAAATGTTGTTGCTG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 28
gtttggcctatttttagaatctaaggatcttgataatacgcgcac---atgcctaatacaacgt-tgtcttacatgttctttatcttttatattct----agGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
    |   |   || || |   |   || |    || || ||      |||  |    |||| | |   ||   |    ||| | ||| ||  | |    |||| || |||||||| |||||||| ||||||||||| || || ||||| |||||||||||||| || |||||||| |||||||| || |||||||| || |
--gggttttggcttaaggagagatttatttcaccaagacacgtgtcctatggattgctcaacctgtaatttgtgtaagatttctatttcattctttgtgtagGTTGTCCGCTGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTCCAGCTTACAGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 25
----------------------------------------------------------------gtttggcc--tatttttagaatctaagg---atcttgataatacgcgcac---atgcctaa-tacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
                                                                 ||||  |  |  || || |||   |||   || | ||    | | |||    ||    ||  ||||| |  |  |     || | | |||      || ||||| ||  | ||||| || ||||| ||||||||||| || || ||||| ||||| |||||||| |||||||| || ||||| || || |||||||||||||
gtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaac-tgatgatgacaattgtgtttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATTAATGTTGTTGCTG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
-----gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatac----aacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
      ||   | |   || ||||   |   || |   |  |     ||||   | |  |     ||  || ||| | ||||    |    ||| | |   |||| ||||||||||| || ||||| ||||||||||| || || |||||||||||||| || || || |||||||| |||||||| || ||||| || || |
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttgtgt---agGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 28
---------gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
            | ||||  | |||   | || | |   |||| ||      |  |    |  | || || ||  | | | |   ||   ||    | |  |||| ||    ||||| || ||||| ||||||||||| || || ||||| ||||| |||||||| || ||| | ||||| ||||  || |||||||||||||
aggtgtatcccatagcctgatatta--ttttatgtaagctgattatgaattgatgtttgaagcataa-gtggtactgcctttcaatttctttcgccaattcagGTTGTCAAATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTCAATATAGCAGCACTTGCTATAAATGTTGTTGCTG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 25
-gtttggccta--------tttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
  |||||| ||        ||| |   | | |   |  |  ||  || | |      | |  |  ||  |||||| | ||||   || || ||  |  | ||||| || || ||||| |||||||| ||||||||||| || || ||||| ||||| ||||| || || |||||||| |||||||| || |||||||| || |
gttttggcttaaggagagatttatttcaccaagacacatgtatcctatg-gattgctcatcttgtaat-ttgtctgagatgtctatt-tcattctttgtgtagGTTGTCCGATGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTCACGGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 25
-------------------------------------------------------------------gtttggc--ctatttttagaatctaaggatcttg-ataat--acgcgcac---atgcctaatacaacgttgtcttacatgttctttatcttttata-ttctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
                                                                    ||||    ||  || || |||   ||| |  |  | |||  | | |||    ||   | |  ||    ||      |   |  || |  |  ||  || ||||| ||  | ||||| || ||||| ||||||||||| || || ||||| ||||| |||||||| |||||||| || ||||| || || |||||||||||||
gttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtagGTTGTCAGATGGGGGCGGTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTTACAGTAAATGTGGCCGCTCTAGTGATAAATGTTGTTGCTG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 27
--------------------------------------------------------------------------------------------------gtttg-gcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
                                                                                                  ||    | |    ||| |  | |  || | ||  | ||      |  |  |    |  | | | ||     |  |  |  |||  | |  | ||||| || || |||||||| ||||| ||||| ||||| |||||||| || ||||| ||||| || || ||||| |||||||||||||||||||| || ||||
gtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaatta-gatatccattttaataatcgtctcat-tcctatagGTTGTCCGTTGGGGTCGATCTGTGTATGCGAATATTCAAAAGTTCATCCAGTTTCAGCTCACGGTTAATGTCGCAGCTCTTGTCATCAATGTGGTGGCTG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
--gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgccta---atacaacgt-tgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
  |    |  |   ||||  |          |||| ||| | |    || | ||   ||||   || | | | |||  ||  ||   ||||    | ||||| ||||||||||| || ||||| ||||||||||| ||||| ||||| ||||||||||| || || ||||||||||||||| | || |||||||||||  
ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgt-tctttatcttttatattct---agGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
                                                  ||| | |||    | |     |  |||  |   |  | |||||   |||| || ||||||||||| || || ||||| ||||| || |||||||| ||||||||||| || ||||||||||  || || ||  |||| || || || |
-------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG

upper sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgt-tctttatcttttatattct---agGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
                                                  ||| | |||    | |     |  |||  |   |  | |||||   |||| || ||||||||||| || || ||||| ||||| || |||||||| ||||||||||| || |||||||| |  || || ||  |||| || || || |
-------------------------------------------------gtaagataacagcttttggtgcgagtctgaaggatcgaaattcttgcagGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCG

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|28188089|gb|CB179699.1|CB179699
EST:     AGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAG                         GTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAG
genomic: AGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAGgtttggccta ... tatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAG
EST: gi|58030120|gb|CX725547.1|CX725547
EST:     AGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAG                         GTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAG
genomic: AGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAGgtttggccta ... tatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAG

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: 48 (upstream exon), 46 (downstream exon)
Score: 106

GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAGgtttggccta ... tatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 123

GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAGgtttggccta ... tatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 102

GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAGgtttggccta ... tatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 85

GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTAGCCAAAGAGAGCTCAGACATAATAATTCTGGATGACAATTTTTCTTCTGTTGTGAAGgtttggccta ... tatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgcacatgcctaatacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG
                       gtcttac  putative branch site (score: 85)
                               tgttctttatctttt  CT-rich tract
                              atgttctttatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgcctaatacaacgttgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC