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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggcaccgtgtaatgacgctcctcgctgctagtgctaccgttctttaatttcttccctgcgaggctgcgactgcgatacgaggtttgctcttgacgtggcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGATGGCGCACGTGGCTCAGTGCGAGATGTTCGCGCTCAATACTGCACTTCA

Basic information

species Zea mays
transcript GRMZM2G036861_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036861_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 12
gtaatggcaccgtgtaatgacgctcctcgctgctagtgctaccgttctttaatttcttccctgcgaggctgcgactgcgatacgaggtttgctct-tgacgtggcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGATGGCGCACGTGGCTCAGTGCGAGATGTTCGCGCTCAATACTGCACTTCA
            |      |||      |   |||    | || | | ||||   ||  |    ||       | |   ||  ||  ||| |||  | |  |  || ||| |||||| ||  ||||||| ||||||||||| || ||||||||||||||||||||||||||| | ||||| || ||||||||  | || ||   ||| || ||
-------acttattctggaacggagggagtacctaaattttccttcccttaaccactcactcatgat------agtataatctgacattttctcaatcaattaactcttgtagCTGTGCCGATGGTGGAGTCCATGGCCGCATTAGTCCTCATGGACCAGCTGATGGCGCACATTGCTCAATGTGAGATGTTTCCACTGAACCTTGCTCTACA
















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|211012763|gb|FL448392.1|FL448392
EST:     CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGGGTCGCCCCTCGAG                         CTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
genomic: CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
EST: gi|16925294|gb|BM078362.1|BM078362
EST:     CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG                         CTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
genomic: CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
EST: gi|148951093|gb|EC896758.2|EC896758
EST:     CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG                         CTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
genomic: CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
EST: gi|78109643|gb|DV528059.1|DV528059
EST:     CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG                         CTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
genomic: CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
EST: gi|76281789|gb|DV021357.1|DV021357
EST:     CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG                         CTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
genomic: CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
EST: gi|148940355|gb|EC885142.2|EC885142
EST:     CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG                         CTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
genomic: CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
EST: gi|76934910|gb|DV174082.1|DV174082
EST:     CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG                         CTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
genomic: CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
EST: gi|149098824|gb|EE184837.2|EE184837
EST:     CGTTGAGCTTTTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAG                         CTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA
genomic: CGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGA

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: 39 (upstream exon), 22 (downstream exon)
Score: 10

GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGATGGCGCACGTGGCTCAGTGCGAGATGTTCGCGCTCAATACTGCACTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGATGGCGCACGTGGCTCAGTGCGAGATGTTCGCGCTCAATACTGCACTTCA


Block sizes: 28 (upstream exon), 49 (downstream exon)
Score: 2

GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGATGGCGCACGTGGCTCAGTGCGAGATGTTCGCGCTCAATACTGCACTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GTGAAACAGAACACCGTGTCAAGGGAGCGTCAGAACGTTGAGCTTCTAGCAAGAGGGCGCCATGACCCATGCGTCGCCCCTCGAGgtaatggcac ... gcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGATGGCGCACGTGGCTCAGTGCGAGATGTTCGCGCTCAATACTGCACTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctgcgaggctgcgactgcgatacgaggtttgctcttgacgtggcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGATGGCGCACGTGGCTCAGTGCGAGATGTTCGCGCTCAATACTGCACTTCA
                                   tcttgac  putative branch site (score: 133)
                                              cttttgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggcaccgtgtaatgacgctcctcgctgctagtgctaccgttctttaatttcttccctgcgaggctgcgactgcgatacgaggtttgctcttgacgtggcttttgcagCTGTTCCTGTGGTGGAATCCATGGCCGCGTTGGTCCTCATGGACCAGCTGATGGCGCACGTGGCTCAGTGCGAGATGTTCGCGCTCAATACTGCACTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG