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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtattatactcgatgtggatatttctaatcaatactttatctttatgcttgcacaaggacctttttcatatgtataagcatgcctgcttgtggtcccatccatggcagacactgctacatgctgtcttatggttttcaatgtttttctttgatatgtcgaatgctgactcagtaagttttgtttcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCTAGTCCTAATTTCGCGGAAGAGGTTGTCACTTTGTTTTTCAAGGACTCGG

Basic information

species Zea mays
transcript GRMZM2G039246_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039246_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g54050.1 (Oryza sativa), 3'ss of exon 1
gcatgtattatactcgatgtggatatttctaatcaat----actttatctttatgcttgcacaaggacctttttcatatgtataagcatgcctgcttgtggtcccatccatggcagacactgctacatgctgtcttatggttttcaatgtttttctttgatatgtcgaatgctgactcagtaagttttgtttcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCTAGTCCTAATTTCGCGGAAGAGGTTGTCACTTTGTTTTTCAAGGACTCGG
||  ||||  || ||  ||  | | ||| |  ||  |    ||  ||   |||||  ||| || ||   | | ||     ||| ||      |||| |  ||    ||||   | ||  |   |    |   |||  || | ||  ||||  |||||||| |  |    |||||| |||| || || | ||| |  | ||||| |||||||||||||||||||| ||||||||||| |||||||||||||||||||||||||| | |||||| ||||| ||||||||||| ||||||||||
gctagtatcctattctctggagttcttttttttccctttcaacagtaatcttatgtgtgctcaggg---tgtgtcgaccatattaggtcttatgctggaagt---gtccacatctgatcccattttcagtattctactgctctttcatgtaattctttgacagat---gtgctgattcagcaaattatattttgatggcagGGATACCTAGATGAGCAATTTTGTCAGGTGGAAGATTTGCAGGATGAAGCTAGTCCTAATTTTGTGGAAGAAGTTGTTACTTTGTTTTTTAAGGACTCGG
















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|211300592|gb|FL372519.1|FL372519
EST:     CTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAG                         GGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCT
genomic: CTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAGgcatgtatta ... tcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCT
EST: gi|211089936|gb|FL388086.1|FL388086
EST:     CTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAG                         GGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCT
genomic: CTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAGgcatgtatta ... tcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCT
EST: gi|211074435|gb|FL412179.1|FL412179
EST:     CTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAG                         GGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCT
genomic: CTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAGgcatgtatta ... tcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCT
EST: gi|88752159|gb|DY536300.1|DY536300
EST:     CTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAG                         GGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCT
genomic: CTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAGgcatgtatta ... tcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCT

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 2 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 9 (downstream exon)
Score: 1

TCCTTCGCCTTGCAACCCTTTGGCTAGTTCATTCATACGAATGGATTATTCTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAGgcatgtatta ... tcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCTAGTCCTAATTTCGCGGAAGAGGTTGTCACTTTGTTTTTCAAGGACTCGG


Block sizes: 39 (upstream exon), 11 (downstream exon)
Score: 3

TCCTTCGCCTTGCAACCCTTTGGCTAGTTCATTCATACGAATGGATTATTCTAATTTGCGTCGCCAAGCTGCATCCATGAAAAAGACTCTCTTTGATCAGgcatgtatta ... tcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCTAGTCCTAATTTCGCGGAAGAGGTTGTCACTTTGTTTTTCAAGGACTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttttctttgatatgtcgaatgctgactcagtaagttttgtttcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCTAGTCCTAATTTCGCGGAAGAGGTTGTCACTTTGTTTTTCAAGGACTCGG
                       tgctgac  putative branch site (score: 3)
                                      ttttgtttc  putative PPT
         tttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtattatactcgatgtggatatttctaatcaatactttatctttatgcttgcacaaggacctttttcatatgtataagcatgcctgcttgtggtcccatccatggcagacactgctacatgctgtcttatggttttcaatgtttttctttgatatgtcgaatgctgactcagtaagttttgtttcgtcgacagGGGTACCTAGATGAGCAATTTTGCCAGGTGGAAGACTTGCAGGATGAAGCTAGTCCTAATTTCGCGGAAGAGGTTGTCACTTTGTTTTTCAAGGACTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG