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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagctgtgaattgtggagcaccgtagcagcttaatagcgcttcatcttcaagatgaattgttgggtgtgatatacattcatgctactttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC

Basic information

species Zea mays
transcript GRMZM2G092719_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g08440.2 (Oryza sativa), 3'ss of exon 1
-tagctgtgaattgtggagcaccgtagcagcttaatagcgcttcatcttcaagatgaattgttgggtgtgatatacattcatgctact-ttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
 | ||   |     | |    | || |||   || |   |||     ||   || |   | |||  | ||| |||| |  |      |  |    ||   ||| |||||||||||||| || |||||||||||||| || || ||||| || |||||||| || |||||||| |||||||| ||||||||||| ||||||||
gtggcatagttgcattgcaacctgttgcaaggta-tgctgctgttcttttgggagggtatcttgaatatga-atacgtgaacatcgttgctgcaattcatagGTATCTACATCATCAACCTCGGCAAGACATGGGAGAAGCTGCAGCTCGCGGCGAGGGTGATTGTTGCCATTGAGAACCCCCAGGACATCATTGTCCAGTC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G17000.1 (Glycine max), 3'ss of exon 1
tagctgtgaattgtggagcaccgtagcagcttaatagcgcttcatcttcaagatga---attgttgggtgtgatatacattcatgctactttt-tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
    | |   || || | | | ||        | |  | |||  |  | ||   ||   ||| | | || |    |  |||  ||    || | ||||| ||||| || ||||| || || ||||| ||||||||||| || || |||||||| || ||| |||| || ||||| |||||||| ||||| |||||||| |||||
---tttttttttttgtaccgctgttatgaag-atttcctcttgctactgaaatagagacattttggagtttttgttgaatttttgtggtttatgtttttttcagGTATTTACATAATTAACCTTGGAAAGACATGGGAGAAGCTTCAGCTTGCTGCTAGGATTATAGTCGCCATTGAGAACCCACAGGATATCATCGTTCAGTC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA15G42150.1 (Glycine max), 3'ss of exon 1
tagctgtgaattgtggagcaccg-tagcagcttaatagcgcttcatcttcaagatgaattgtt---gggtgtgatatacattcatgctactttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
  |  ||    | |   |||||| || ||      |  |   |        | ||  |   ||   | || |    |  |||  ||    || | |||  ||||| || ||||| || || ||||||||||||||||| || |||||||| || || ||| |||| |||||||| |||||||| ||||| ||||| || |||||
--ggcgtttgcttttttgcaccgctaccatgaaggtttcctcttgctactgaaatagaacattttggagtttttgttgaatttttgtggtttatgttt--tcagGTATTTACATAATTAACCTTGGCAAGACATGGGAGAAGCTCCAGCTCGCTGCTAGGATTATTGTTGCCATTGAGAACCCACAGGATATCATTGTTCAGTC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G01460.1 (Glycine max), 3'ss of exon 1
-----------------------------------tagctgtgaattgtggagcaccgtagcagcttaatagcgcttcatcttcaagatgaattgttgggtgtgatatacattcatgctactttttttttg---tcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
                                   | | |   ||   |  |   |  | |  | || |    ||   | ||  || |       |    | |||| |   ||  ||    ||   ||| |   | ||| || ||||| || || ||||| ||||||||||| || || ||| | ||||| |||||||| ||||| || |||||||| ||||| ||||| || || ||
gtaactgaacttttctcgttctctcttttatcatctcgttaaaaaaattaaatttcaatggatgtttgaatctgcaatagctgtaatagaggaattgaattttgatttgatttggtgtggtttggatttgggaattagGGATTTACATTATTAACCTTGGGAAGACATGGGAGAAGCTTCAGTTAGCAGCTAGGGTTATTGTTGCAATTGAGAACCCTCAGGATATCATTGTTCAATC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT1G72370.2 (Arabidopsis thaliana), 3'ss of exon 1
-tagctgtga-attgtggagcaccgtagcagcttaatagcgcttcatcttcaagatgaattgttgggtgtgatatacattcatgctacttttttt--ttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
 ||  ||||  | ||||    |  || ||   || || |      || | |||    || || || || ||  |   | |  |   | ||||  |  || ||||| || |||||| |||| |||||||| |||||||| || |||||| | || || || ||||| |||||||| |||||||| ||||||||||||||||||||
gtatttgtgctagtgtgtgttattgttgctcttttattgta----atttacaattgtaagtggtgagtatggaacttagtttttgaagttttcgtcattctcagGTATTTACATCTTCAACCTTGGCAAAACATGGGAAAAGCTCCAGATGGCTGCTAGAGTTATTGTTGCCATTGAGAACCCACAGGACATCATCGTCCAGTC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 3'ss of exon 1
--tagctgtgaattgtggagcaccgtagcagcttaatagcgcttcatcttcaagatgaattgttgggtgtgatatacattcatgctactttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
   | ||| | |   |         |    | | |   |   |  |  |   | |||| ||  ||       | ||   || |    |||| |  |  ||||| || ||||||||||| ||||| || |||||||| || || ||||||||||| ||||| || ||||| || ||||||||  |||||||||| || |||||
accatctgcggaaaataacatgatttgatggatgatcggttttgtagatatgaaatgattt--tgccaaaattttaagatcttttgtctttctaatgatcagGGATTTACATCATCAACCTTGGAAAAACATGGGAGAAGCTGCAGCTTGCAGCCAGGGTGATTGTTGCGATTGAGAACCCTAAGGACATCATTGTTCAGTC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S173_16V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------------tagctgtgaattgtggagcaccgtagcagcttaatagcgctt-catcttcaagatgaattgttgggtgtgatatacattcatgctacttt------ttttttgt-cagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
                                                                                             | |  |   ||  ||     ||      ||    | |  |  || ||   || |  | || |  || | |        ||  |   ||      |   |||  |||| || | |||||| ||| | || ||||| |  || || ||  |||| || |||||||| || | ||||||||||||||| ||||||||||| || |||||
gtgagaactctgtcccctccattgtttgtcctcgtcccggtgtgttatcggtgtgggcttggggtgagaagtttctgtgttatgaatgataagggttcggggtgaagatacaagtttttttttggacgtgtgtatatgttttggacgggtcgtggtttggggtggttgactattgtggcttggcgggtccgttgcgcagGTATTTTCATCATTAATGTGGGAAAGACTTACGAGAAGCTGGAGCTGGCGGCGAGGGTGATTGCTGCCATCGAGAACCCTCAGGACATCATTGTGCAGTC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S209_48V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------tagctgtgaattgtggag-caccgtagcagctt-------aatagcgcttcatcttcaagatga---attgttgggtgtgatatacattcatgctactttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
                                                               | | | |    || || | |  ||  |  | ||        || |   |   |  | ||| ||    ||||  | | ||  |            |  || | | | | ||||||| | |||||||||  | |||||||| |  || || ||  |||| || |||||||| || | ||||||||||||||||||||||||||||||||||||
gtaattagggctttttccccctgtggcccgtgttggggtttggttgggtgcgtgtgcgagtgttcgttttttggtgcgggggcggcgcggggggtttggtgcggatggaattggtttgtgaaggtgggcgattgacgagggtagtggggtcgttgttttattctgtgtgggcagGCATTTTCATCATCAACGTGGGCAAGACCTACGAGAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------------------tagct-gtgaattgtggagcaccgta-gcagc----ttaatagcgcttcatcttcaagatgaattgttgggtgtgatata-cattcatgctactttttttttgt-cagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
                                                                                     | | |   | || |  | |||  | | |||||    ||  || || | | |      | ||   |   |  ||||   |   |   |||        |   ||  ||||||| |  || |||||  |||||||||| |  || || ||  ||||||| |||||||| || |  ||||||||||||||||||||||| ||||| |||||
gtattaattctcattagggttattccttagacaatttctagttgtggaatgggctcggtgtcgtcgttgtcgtcgtcttcttgcttggtttacggatgggtgcgcaatgcatgcagcgttgttcgtaacgttgcgtgccggtgctgccctccggtatgtgtggtggtaacaatgtggtcgcatcggtggacagGCATTTTTATTATCAACGTTGGCAAGACCTACGAGAAGCTTGAGCTTGCTGCGAGGGTGATTGCGGCCATCGAGAACCCGCAGGACATTATCGTGCAGTC

upper sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S48_103V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------tagctgtgaattgtggagcaccgtagc--agcttaatagcgcttcatcttcaaga-tgaattgttgggtgtgatat--acattcatgctactttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
                                                            | | | |   |    | || | |  |    | |     |    |  | |   | | ||   |||||     | ||   || |   |  |  |||| | | | |||| || | |||||||||| | |||||||| |  || || ||  |||| || |||||||| || | ||||||||||||||| ||||||||||||||||||||
gtaattagggtttttcctcctgtggcccgttggggtttggttaggtgcttgtgcaagtgttcgtttttggtgcgagggcgcgggggtttggttcggagggaagtggtttgtgatagtgggctgttgacgagggtagtgacgtcgttttttattttgtgtgggcagGTATTTTCATCATCAATGTGGGCAAGACCTACGAAAAGCTGGAGCTGGCCGCGAGGGTGATTGCTGCCATCGAGAACCCCCAGGACATCATCGTCCAGTC

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|29544407|gb|CB604787.1|CB604787
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|149000198|gb|EE037342.2|EE037342
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|30306899|gb|CD001572.1|CD001572
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|28361631|gb|CB239987.1|CB239987
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|148982964|gb|EE028852.2|EE028852
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|28931357|gb|CB334718.1|CB334718
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|4681187|gb|AI629857.1|AI629857
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|22545631|gb|BU097990.1|BU097990
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAGCGCCGTTCCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|31910443|gb|CD651426.1|CD651426
EST:     CTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: CTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|28361815|gb|CB240171.1|CB240171
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
EST: gi|30087521|gb|CB885727.1|CB885727
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         T
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcag-
EST: gi|30087521|gb|CB885727.1|CB885727
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         T
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcag-
EST: gi|50330906|gb|CO526032.1|CO526032
EST:     GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACG                         GCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG
genomic: GAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAG

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: 103

GAGCAGGACATACAGATGATGCTCGCCGCCGACGTCCACCTTGGCACCAAGAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 70

GAGCAGGACATACAGATGATGCTCGCCGCCGACGTCCACCTTGGCACCAAGAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

GAGCAGGACATACAGATGATGCTCGCCGCCGACGTCCACCTTGGCACCAAGAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 83

GAGCAGGACATACAGATGATGCTCGCCGCCGACGTCCACCTTGGCACCAAGAACTGCGATTTCCAGACGGAGCGCTATGTCTTTAAACGCCGCACCGACGgtatgtgcct ... tttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaagatgaattgttgggtgtgatatacattcatgctactttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC
                                     ctactttttttttgtc  CT-rich tract
                                      tactttttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagctgtgaattgtggagcaccgtagcagcttaatagcgcttcatcttcaagatgaattgttgggtgtgatatacattcatgctactttttttttgtcagGCATCTACATCATCAATCTTGGCAAGACATGGGATAAACTCCAGCTTGCAGCGAGGGTTATCGTTGCCATCGAGAACCCGCAGGACATCATCGTCCAGTC

- - - tgaattg
- - - - - - -tggagca
- - - - - - - - - - - - -gcagctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - attgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcatgc