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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaaggatgtcgccattttttgcagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC

Basic information

species Zea mays
transcript GRMZM2G359234_T01
intron # 1
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 1
gggaaggatgtcgccattttttgcagcatgtgt-ccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
        | | || | || ||     || |   | ||| |  ||  |   |  || ||  | | | |  | || ||| |||  ||||||||| ||  |||||||| |||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||| | ||||||||||||||||||||||| ||||| |
-catgtttttttgcaacttattatgttattttcactatttacaatataatcatgtgttgcatctgtatattatcaaatctgggtttcttaacaattattacAAGACCAATGTCATGGGAACCTTGAATATGTTGGGTCTGGCAAAGCGAATTGGTGCAAGGTTCTTGCTAACTAGCACAAGTGAAGTTTATGGAGATCCAC

upper sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 1
-------gggaaggatgtcgccattttt-tgcagcatgtgtcca----ttcagtatccatatagatggtgtgtttcttttgtctcgaatt-tggacttcttaacactttgt--acAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
        |    |||||    | | |    |||| | | |       |  | || |  | |    |   | ||| |||||  | || || ||   | |||||   || ||  ||||||| ||||| ||||| ||  | || ||| | || || |||||||||||||| || |||||| || | ||||| || ||||| ||||| ||||||||||
atatccttgtctcgatgttctaactctaactcagcgttttttttaagttctaataactcttttttcgtaatttttattttgcgttgagttctgtgatccttaattattagtttacAAGACGAATGTGATGGGCACGCTTAACATGCTTGGCCTTGCGAAGCGAATTGGGGCTAGGTTTCTGCTTACTAGTACTAGTGAGGTTTACGGTGATCCGC

upper sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 1
----gggaaggatgtcgccattttttg-cagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggac--ttcttaacact--ttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
       ||  ||   |  ||||  ||     |||| ||||||  | ||   | |   |  | | ||  |  | |   || | |||    | ||||||  |  || |||||||||||||| ||||| ||| | |||||||||||||| || ||| || |||| ||||||||| || | || |||||||||||||| ||||| |      
ctcttacaattattgtgatatttcgtgatgaaatgtttccattgggaatgtgttt---ttctctattgttgatatgatgattctggttgatccttaaccatagTTTTACAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAG------

upper sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G53520.1 (Arabidopsis thaliana), 3'ss of exon 1
gggaaggatgtcgccattttttg-cagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggac--ttcttaacact--ttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
   ||  ||   |  ||||  ||     |||| ||||||  | ||   | |   |  | | ||  |  | |   || | |||    | ||||||  |  || |||||||||||||| ||||| ||| | |||||||||||||| || ||| || |||| ||||||||| || | || |||||||||||||| ||||| ||||| |
--caattattgtgatatttcgtgatgaaatgtttccattgggaatgtgttt---ttctctattgttgatatgatgattctggttgatccttaaccatagttttacAAGACAAATGTAATGGGCACTCTCAATATGTTGGGTCTTGCAAAGAGAGTTGGGGCAAGGTTTCTGCTCACCAGCACAAGTGAAGTCTATGGAGATCCCC

upper sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 2
gggaaggatgtcgccattttttgcagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttg--------tacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC---
       | |  ||||  |  || |  || |    |||||  | ||| ||  | ||| |  |  ||||||    ||||||||  ||||    | |||        |||||||||||||| ||||| ||  |||| |||||||| || || ||| | ||||| |||||||||||| | || || |||||||||||||||||||| || |   
-------agggtgccaaatgatgaataatttagg-attcaaaaaccaaatgtaaggt-tagtgattttgtg--aaatttggatctcttttatccttgactgtgattacaagACAAATGTGATGGGCACCCTGAACATGTTGGGCCTTGCAAAGAGGATTGGGGCAAGGTTTTTGCTCACAAGTACAAGTGAAGTTTATGGTGACCCCCTTG

upper sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S120_28V6.1 (Physcomitrella patens), 3'ss of exon 1
gggaaggatgtc-gccattttttgcagc----atgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttgt-acAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
    |  | ||| |   || |  || ||    | | ||  |    || | |||  |  |   |        |  |   |||      || ||||||      | ||||||| |||||  ||||||| ||||| ||||||||  |||||||||| ||||| ||| | || ||| |||| ||||||||||| ||||| || |||||  
-tccacaacgtctggtcttctgcgcggctctcacgcgtagaagtcgt-ttcattcacttcaagaaggataatctttgtgaacc----ctccttaacttaccatcacAAGACCAATGTGGTGGGAACATTGAACATGTTGGGATTGGCGAAGCGGATTGGAGCACGATTCTTGCTGACCAGCACAAGTGAGGTTTACGGCGATCCTT

upper sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------gggaaggatgtcgccattttttgcagcatgtgtc-cattcagtat-ccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactt-tgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
                                       | ||     | ||  ||||     | |||| || | ||  || | |  || ||| | ||| ||   || |||     |  || |  |||||   |  |  ||||||| || ||  |||| || ||||| ||| ||||  |||||||||| ||||| ||| |||| |||||||| || || ||||| ||||||||||||||  
atatccttttttgtgcgagatcttgtgtgttatgaatctgaaatccccttgcgtttttcctatgaatgtctcacgttttgtttgctgtagagaagatgttttcgattcgtcattcgtgcggcccccttaatcttcctacacAAGACCAACGTGGTGGGGACCTTGAACATGCTGGGATTGGCGAAGCGCATTGGAGCACGGTTCTTGTTGACCAGTACGAGTGAGGTTTATGGTGATCCTT

upper sequence: GRMZM2G359234_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ30517 (Selaginella moellendorffii), 3'ss of exon 2
-----gggaaggatgtcgccattttttgcagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttg------tacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC---
     |   |  || ||    | || |        | | | ||   |      ||  |  | |||||| |||| | |     |||   | |||||| ||| |       ||||||| || ||  | |||||  | || ||| | ||  |||| ||||||||||||||  |||||||| |||| |||||||| || |||||||| |||||||   
gtcaagacgatcatatccttttcttctttgcttgttcttcgtttgtttcgagcatctaacgcgtgttttttttttttttttgttgc-ttccttaactcttggagctttcacaagACCAACGTGGTTGGAACACTCAACATGCTCGGATTGGCCAAGCGAATTGGTGCTCGGTTTTTGCTGACCAGCACAAGCGAGGTTTATGGAGATCCGCTGG

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|32808730|gb|CD960964.1|CD960964
EST:     CGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATC                         AAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATT
genomic: CGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATT
EST: gi|78125737|gb|DV544121.1|DV544121
EST:     CGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCACTCAAGACGATC                         AAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATT
genomic: CGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATT

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), 46 (downstream exon)
Score: 105

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 411

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 467

CGATGTAGTCGAGCCAATCCTCCTCGAGGTGGACCGGATCTACCACCTCGCGTGCCCCGCGTCGCCTGTGCACTACAAGTACAACCCAATCAAGACGATCatatccttca ... cactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC
                                     cttcttaac  putative branch site 
               tttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggaaggatgtcgccattttttgcagcatgtgtccattcagtatccatatagatggtgtgtttcttttgtctcgaatttggacttcttaacactttgtacAAGACAAATGTCATGGGAACTTTGAATATGTTGGGTCTGGCGAAGCGAATTGGTGCAAGGTTTTTGTTGACTAGCACAAGTGAAGTTTATGGTGATCCGC

- - - - - - - - - - ttgcagc
- - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - -gatggtg