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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA

Basic information

species Zea mays
transcript GRMZM2G084347_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
----gagtcttatcagccatggtccaaaaggaagccca-tactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA------
       | | ||   | |||| |||||| | |||||   |||  | ||| | ||| |||||| | || || |||||| | | |  ||| | |       |||||||||| || ||  | || ||||||||||| || |||||||| |||||||| ||||| || ||||| |||||||||||      | | |||| | || |||      
ggtctcatttgatttactatggcccaaaatggagcccggcactctcttaatgtaaattttgcaatgtctctaatttgtcccatttatttatatct-----tacagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGT------CTCTTTGGTTTCTACAAATCACA

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G10470.1 (Glycine max), 3'ss of exon 6
gagtcttatcagccatggtccaaaaggaagcccat----actaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
 | |||   |        |      ||    |||     | |    || |  | |  ||  | |      ||   ||| ||||  |    |   |||| | |||| | || || | || || ||| ||||||||||||||||||| || ||||| ||||| || || |||||||| ||  | ||    || |||| | ||||| 
-attctccccttgtggaattttttgggctatccaagataattgtgttatattacagcttctattcgtatagaacagtgttaatgttcagct---cttactgcagAGACGACGGCTGATCACACATTCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
gagtcttatcagccatg-gtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttc-cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
   | |    |   ||   |  | |     |        |      |||  |||||    | ||      ||||  ||||  ||  ||  | |||| |||||| | |  |  |  | || |||||||||||||||||||||||||| ||||| ||||| || ||| |||||||  |  | ||    || |||| | ||||| 
atatatatatatatatatatatatacatggggttggttcatatctcagcttactttt--atgtcttaatcttgtagtaatggttgcttaactcttattacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
gagtcttatcagccatggtccaaaaggaagcccatactaccat---aaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
|  | || |  |      |      |  | || | |  |   |   | |  | |  ||    ||  |  ||   ||| ||||  |    |   |||| | |||| | |  || | || || ||||||||||||||||||||||| || ||||| ||||| || || |||||||| ||  | ||    || |||| | ||||| 
gtatattctacgtggaaattttggggttatccaagataattgtgttatattacagcttttcttagtgtagaacagtgttaatgttcagct---cttactgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagt-atcgctgatttgtgctaatcctttt--ttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
                                                                | || | |  |   |  |  ||  | ||  |  ||  |   | |   ||| | |  | | |  | |||||     |        |  |||    |   ||||| |||  | || || |||||||||||||||||||||||||| |||||||| ||||| |||||| |||||||   | ||||  | || ||||   |||| |
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgtt-ttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 6
gagtcttatcagccatggtccaaaaggaagcc-catactac--cataaagc--aaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
    || ||      |     | || | | |  |||  ||   |||  ||   |||||    ||||  | | |  | || || |    ||| |||  ||  ||||| |||| |  | || |||||||||||||| ||||||||||| |||||||||||||| ||||||||||||||    |||||| | || ||||   ||||| 
---actgatttattttacaatacaaagtatctgcatgataatgcatccagtcaaaactcaaaagtaaagattaaatttgttactatgatttcttctgta--acagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTGGGATCTTCAC

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
gagtcttatcagccatggtc---caaaaggaagcccatactaccataaa-gcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
   ||| || | |  |  |    ||| || |||   || |    |||       | |    ||||  | | |  | || || |    ||| ||   ||  ||||| |||| |  | || |||||||||||||| |||||||||||||||||||| ||||| ||||||||||||||    |||||| | || || |   ||||| 
--ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgta--acagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
----gagtcttatcagc-catggtccaaaaggaagcccatac-taccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
     |||   ||||    ||      | | | ||    | | || |  ||  |  |||||   || |   |   ||||  ||||  |||   |  |||| |||||| | |  |  |  | || ||||||||||||||||||||||| || ||||| ||||| || ||  |||||||  |  ||||    || |||| | ||||| 
cataaagtggcatcaatatatatatatacatggagttggttcatatctcaa--cttacttttatgtcttaata--ttgtagtaatggtttaact--cttattacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcag-tatcgctgatttgtgctaatcctttt--ttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
                                                              |   | || | |  |  |   |  | ||  |  ||      | |   ||| | |  |  || || |||||     |        |  |||    |   ||||| |||  | || || |||||||||||||||||||||||||| |||||||||||||| |||||| |||||||   | ||||  | || ||||   |||| |
gtatgttaaagaaatttacttctattgttttatgcctttgaactgctgctttccttctaataaaattcattatcatttttattattgaaaatctgtatagttgtgattgaaagtataaaactaacgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
---gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTG---CGGTTGGTGTCCCCTTGGATGCTTCAA
   |  |||       |    | || |   |  | || ||   || | |   | | ||    | |  |  | |  |    ||| |||   |     ||  |||| ||| || || || || || |||||||| |||||||||||||| ||||| || || ||||| ||||||||||   |  | ||||| || |||| ||| |   
tctgcttctagcatatctacatacacacacacacacacacacacaaagactgatccttt---ttttacataatcatttctatcttttgactcttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT---

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
------gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTG---CGGTTGGTGTCCCCTTGGATGCTTCAA
      |  |||       |    | || |   |  | || ||   || | |   | | ||    | |  |  | |  |    ||| |||   |     ||  |||| ||| || || || || || |||||||| |||||||||||||| ||||| || || ||||| ||||||||||   |  | ||||| || |||| ||      
tgttctgcttctagcatatctacatacacacacacacacacacacacaaagactgatccttt---ttttacataatcatttctatcttttgactcttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG------

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
gagtcttatcagccatggtccaaaaggaagcccat-actaccataaagcaaac-tttgcagtatcgctgatttgtgctaat-ccttttttttcc---ttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
   | | ||||    |||  | | |  |      | |  |   |    |  |   ||| ||| | |  |||||    |  |  ||| | | |||   |  | |||||   || |  | || |||||||||||||| ||||||||||| |||||||| ||||||||||| || |||||  |  ||||   ||| |||| | ||||| 
---tttcatca--tgtggctccatataattttgttgatcaagttggttctgatacttgtagt-ttgtagattttgattgctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC

upper sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 9
----gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
    |||  ||     |  |  |      | || | |      || |  | | |   ||  | | |     ||||||     ||| | ||| |   | | ||||  |||| |  | ||  | ||||||||||| ||||| ||||| |||||||| ||||| || || || || || || |||||  ||||||||| ||||||| 
ttgagagcttttgtttcttttttatgtttgcaatcacccgagtccttgcaaccagagttcgattgtt-tgaatttgttt---tccgtgtttctttctgaaacagCGAAGACGCCTAATCTCCCATGCAAATGCAAAGAGTAAGAGTGAAAAGTTTCCTCCACCTCACCAGGACGGAGCAGTTGGCTTCCCCTTGGGTGCTTCAC

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|12046405|gb|BF728544.1|BF728544
EST:     AGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGAT                         AAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
genomic: AGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
EST: gi|71762487|gb|DR960424.1|DR960424
EST:     GCAGTTCCAGCTCCAGAGGCAAATGGTGAACTTCAAGTAAATATTGAT                         AAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
genomic: GCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
EST: gi|76013924|gb|DT941094.1|DT941094
EST:     AGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGAT                         AAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
genomic: AGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
EST: gi|71332957|gb|DR803507.1|DR803507
EST:     AGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGAT                         AAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
genomic: AGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
EST: gi|149086047|gb|EE175576.2|EE175576
EST:     AGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGAT                         AAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
genomic: AGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC

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: 46 (upstream exon), 48 (downstream exon)
Score: 35

TAGAGCTAATGGTGATGGAGCCAAGAAGACGAGAACACGTGATCGACCTAAGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 14

TAGAGCTAATGGTGATGGAGCCAAGAAGACGAGAACACGTGATCGACCTAAGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 33

TAGAGCTAATGGTGATGGAGCCAAGAAGACGAGAACACGTGATCGACCTAAGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 16

TAGAGCTAATGGTGATGGAGCCAAGAAGACGAGAACACGTGATCGACCTAAGGCAGTTCCAGCTCCAGAGGCAAATGCTGAACTTCAAGTAAATATTGATgtatgttgaa ... cttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
                           tgctaatccttttttt  CT-rich tract
                                    ttttttttccttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtcttatcagccatggtccaaaaggaagcccatactaccataaagcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - -gccatgg
- - - - - - - - - - -aaaaggaa
- - - - - - - - - - - - - - - -ccatact
- - - - - - - - - - - - - - - - - - - - - - aagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatt