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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgacctcctcccacccacctcttctatttctgtttatttatgtatctagactgaaattttgaattcttggtaggagtctaggagagtatttgctaacactgatggcattgtgcaatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATCTAACTGACTCTGCCTAAGCTCAACCGGAAGGCATGGCCATAAGCTGAAG

Basic information

species Zea mays
transcript GRMZM2G069816_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069816_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 9
gcatgacctcctcccacccacctcttctatttctgtttatttatgtatctagactgaaattttgaattcttggtaggagtctaggagagtatttgctaacactgatggcattgtgcaatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATCTAACTGACTCTGCCTAAGCTCAACCGGAAGG--CATGGCCATAA-GCTGAAG
                  ||      | | | ||||| |||||| ||||      ||| || | || | ||| |||              ||||||| |   ||      ||||   |||||||||||||| ||||||||||| ||||||||||||||| |||||||| |||  || |||||||   || | |||  | | |||  |   | ||  | |  ||| || 
-----------------gcatgatccccaatcctgttcatttatttatcg-----gaagttctaaaatattg-tag--------------atttgctgatcttggcac--ttgt---atgttcagGGTGAGCCCTTCTAAGACACCGGTGAAGCCACGTTTAAATCGAGTGGCGTCGAACTGACC--GCTTGAGCCAAGCTGGATTGTTTACGGGAAGATCGCTTAA-
















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|211272638|gb|FL458520.1|FL458520
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAG                         GGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
EST: gi|149096649|gb|EE182415.2|EE182415
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAG                         GGTGAGTCCTTTTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
EST: gi|166441067|gb|EG075559.1|EG075559
EST:     GGGAACTCTGCCTGTTAG                         GGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
genomic: GGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
EST: gi|78179282|gb|DV549655.1|DV549655
EST:     GAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAG                         GGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
genomic: GAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
EST: gi|60352077|gb|DN219050.1|DN219050
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAG                         GGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
EST: gi|211064466|gb|FK995272.1|FK995272
EST:     ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAG                         GGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC
EST: gi|78092728|gb|DV521102.1|DV521102
EST:     ATCATGGTTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAG                         GGTGAGTCCTTTTAAGACTCCGGTGAAGCCACGTGTAAATGGAATGGGATC
genomic: ATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATC

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: 102

GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATCTAACTGACTCTGCCTAAGCTCAACCGGAAGGCATGGCCATAAGCTGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 113

GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATCTAACTGACTCTGCCTAAGCTCAACCGGAAGGCATGGCCATAAGCTGAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 90

GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATCTAACTGACTCTGCCTAAGCTCAACCGGAAGGCATGGCCATAAGCTGAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 80

GCTGAGGGTGCCATCATGGCTCTGAATTGCAGCGGGATGATTTTGGGAACTCTGCCTGTCAGgcatgacctc ... caatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATCTAACTGACTCTGCCTAAGCTCAACCGGAAGGCATGGCCATAAGCTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtaggagtctaggagagtatttgctaacactgatggcattgtgcaatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATCTAACTGACTCTGCCTAAGCTCAACCGGAAGGCATGGCCATAAGCTGAAG
                 agtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgacctcctcccacccacctcttctatttctgtttatttatgtatctagactgaaattttgaattcttggtaggagtctaggagagtatttgctaacactgatggcattgtgcaatgttcagGGTGAGTCCTTCTAAGACTCCGGTGAAGCCACGTGTAAATCGAATGGGATCTAACTGACTCTGCCTAAGCTCAACCGGAAGGCATGGCCATAAGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG