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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC

Basic information

species Zea mays
transcript GRMZM2G116151_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g11140.2 (Oryza sativa), 3'ss of exon 13
----gtcaagctgcg-attgcaagcttttagctggaggctgtgacagtttat-ggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
    ||     ||   || | ||| || |      ||| |  |      | | | |||| |||| | |  | |  | |||| || || ||| ||||  |     ||| || ||||||||||| ||||| |||||||||||||||||||| || ||||||||||||||||| || |||||||||||||| ||||| |||||||||||
attagttggtgtgtacatggaaagtttgtgtgcacaggatacgttcccctgttgttattacactagcatgtcc-ttatagattgtaactgattttgagc-----agGGACGCAATATGCCCAACAATCCTACAAAGTAAGCGACTCATTTCCCTTCAAGTGGATAAACAAGAAGTGGAAGGAGGGTTTCTATGTCACTGCTATGGC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA04G09070.2 (Glycine max), 3'ss of exon 13
----------gtcaagctgcgatt----gcaagcttttagctggaggctgtgacagtttatggtattgcacttgt-------agatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
           | ||| |   |||          | |    | | ||  |  | | | ||     ||  ||| ||       | ||   ||    | | | |||    |||  |  |  ||| || || ||    |||||||| || ||||| || || || || || || |||||||| |||||||||||||  || || |||||||| |||||||||||
gttaatacccctgaagtttttattcttcatgtattgtgtatttggggtggcaataatatacatattttgactggttatgtttaaattgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTACAGCAATCCTATAAAGTCAGTGATTCGTTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 13
----------------------------------------gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtaga-----------tacactgtag----aatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
                                         |      |||||     ||||     | || |   | |||  || || | |||||  | | ||           || |||||      | | | |||    |||  |  |  ||| || || ||    |||||||| || ||||| || || ||||| || || |||||||| |||||||||||||  || || |||||||| |||||||||||
gttaatcccctgaagtatttattcttcatgtattgtgtctttgggatggcgataattggcttgagtttagatg--atcacatgttttgcttttgcatattttgactggttatgtttaaactgtcttcttacttgtatttggattgatccttttagGTACCCAGTACTTGCAGCAATCCTATAAAGTCAGTGATTCATTTCCATTTAAGTGGATCAACAAAAAATGGAGAGAAGGATTTTATGTCACTGCTATGGC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 13
gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
     | |   |   | |   | ||  |   |||  || || |||     ||| || || |   |   | |  || |     |||  |||  ||  ||||| ||||| |||   |||||||| || ||||| || |||||||| |||||||||||||| |||||||| |||| |||||| ||||| || ||| | |||||
-----gttagtacctctaaagtata--tattggcaatgtcaatttggcaaatttcaattttg--ttttccgctgacta----tgatcttggact--ccagGCACACAGTATTTGCAGCAATCATATAAAGTTAGTGACTCATTTCCTTTCAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTTCAATGGC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 13
gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
       |    ||  |  | ||| |   |  | ||| ||||||  |    ||  |  |         ||||   |  |  || |   | |  | | |||| || || |||   || ||||| |||||||| || || || || || |||||||||||||| ||||| |||| ||| || |||||||||||  | |||||
---gtattcttgttttactccttttgaatgcaggtgtaacagttatttccgttttatct---------ctgtttcacagttttcatcat-ttgtattcagGGACCCAGTATTTACAACAATCCTACAAAGTCAGTGATTCTTTTCCCTTCAAGTGGATAAATAAAAAGTGGAGGGAAGGGTTTTATGTTACATCAATGGC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 13
gtcaagctg--cgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
||||   ||    |||  || |   |   |    |     |    || |  |||     || |   | | || |  |      || | |||      |  ||| || ||||||   ||||| || || ||||| || || ||||| || || ||||||||||| ||||||||||  |||||||| |||||||||||||||||
gtcagtgtgacttatttaaaaccaatcattttttgagacaatgacttcttttatgattgttatctgt-ctcttttaacctctgttaa-tttactgaatatagGCACGCAATATTTACAGCAGTCCTATAAAGTCAGTGAGTCATTTCCATTTAAGTGGATAAATAAAAAATGGAGAGAGGGTTTCTATGTTACTGCTATGGC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 13
gtcaagctgcgattgcaagct-tttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
        |  | |  ||  | ||| ||||  || | |       ||||  |    | || |  |||   ||     | || || | ||  |   ||||||| ||||||||    || || ||||||||||| || || ||||| || |||||||||||||| |||||||||| ||||||||| ||||| ||  |||||||
--------gttagtctaacatatttggctgatggattt------ctatgaca--aaatttatctatattttgc----ttgacttcatttcattgactccagGTACACAATACTTGCAACAGTCTTACAAAGTTAGTGATTCATTTCCCTTCAAGTGGATAAATAAAAAATGGAGGGAGGGTTTCTATGTCACCTCTATGGC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatgga-attgac---tttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
                                              |  | | ||  || | |||   |  | | || |    ||||   | | ||| |  |||| |||| |||  | || ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| |||| ||| || ||||| || ||| | |||||
---------------------------------------------gtattgtcgctgttattgatggccactggcattgtcgctgacgcgtgtttcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatgga-attgac---tttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
                                              |  | | ||  || | |||   |  | | || |    ||||   |   ||| |  |||| |||| |||  | || ||||| |||||||| ||||| ||||| || ||||||||||| |||||||| |||| ||| || ||||| || ||| | |||||
---------------------------------------------gtattgtcgctgttattgatggccactggcattgttgctgacgcgtgattcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

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|31357223|gb|CD441580.1|CD441580
EST:     GCGCTAGCAGGGGCAACCAATGGTAGTTCACTGGTGGTCATGTCGAGAG                         GAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCA
genomic: GCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAGgtaatacaat ... tcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCA
EST: gi|89248581|gb|DY620367.1|DY620367
EST:     TGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAG                         GAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCA
genomic: TGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAGgtaatacaat ... tcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCA
EST: gi|67013328|gb|CO442077.1|CO442077
EST:     TGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAG                         GAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCA
genomic: TGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAGgtaatacaat ... tcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 97

GAATGGATAATGGAACAATGGGAGAAGAACTTCTATATCACTGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAGgtaatacaat ... tcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

GAATGGATAATGGAACAATGGGAGAAGAACTTCTATATCACTGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAGgtaatacaat ... tcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

GAATGGATAATGGAACAATGGGAGAAGAACTTCTATATCACTGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAGgtaatacaat ... tcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC


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

GAATGGATAATGGAACAATGGGAGAAGAACTTCTATATCACTGCGCTAGCAGGGGCAAACAATGGTAGTTCACTGGTGGTCATGTCGAGAGgtaatacaat ... tcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC
                                  aattgac  putative branch site (score: 48)
                                        ctttgtcctctcc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaagctgcgattgcaagcttttagctggaggctgtgacagtttatggtattgcacttgtagatacactgtagaatggaattgactttgtcctctccagGAACACAATATGCCCAGCAATCTTACAAAGTAAGCGACTCATTCCCTTTCAAGTGGATAAACAAAAAATGGAAGGAGGGTTTTTATGTTACTGCTATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- -aagctgc
- - - - - - -tgcaagc
- - - - - - - - - - - - -gctggag
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcactt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacactg