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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgcgctcacgctccgtttgcttgtgatccgtcccgtgcacgctttctgtttgatcaaattccctggcgtgtttcaccatctgtgcttgacacgatgagttggttggtgttgtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG

Basic information

species Zea mays
transcript GRMZM2G305007_T01
intron # 1
splice site 3'
intron type U2

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|211098338|gb|FL317179.1|FL317179
EST:     CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAG                         CTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGG
genomic: CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAGgtccgcgctc ... gtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGG
EST: gi|211541628|gb|FL367733.1|FL367733
EST:     CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAG                         CTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
genomic: CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAGgtccgcgctc ... gtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
EST: gi|148941497|gb|EC886426.2|EC886426
EST:     CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAG                         CTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
genomic: CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAGgtccgcgctc ... gtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
EST: gi|149069689|gb|EE158073.2|EE158073
EST:     CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAG                         CTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
genomic: CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAGgtccgcgctc ... gtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
EST: gi|31359132|gb|CD443489.1|CD443489
EST:     CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAG                         CTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
genomic: CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAGgtccgcgctc ... gtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
EST: gi|211152953|gb|FL361223.1|FL361223
EST:     CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAG                         CTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
genomic: CGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAGgtccgcgctc ... gtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG

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: 48 (upstream exon), 36 (downstream exon)
Score: 3

CGTGCTCCGCCGCTCCCTGCAGATCGGCACCTCCTTCGGCCGGTGGTTCGCGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAGgtccgcgctc ... gtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG


Block sizes: 43 (upstream exon), 41 (downstream exon)
Score: 5

CGTGCTCCGCCGCTCCCTGCAGATCGGCACCTCCTTCGGCCGGTGGTTCGCGCTGCGGTACCTCGATCGCGTCAACGAGCGCGCCGACGACATGTTCGAGgtccgcgctc ... gtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtgtttcaccatctgtgcttgacacgatgagttggttggtgttgtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG
                  gcttgac  putative branch site (score: 5)
                                           ttgtcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgcgctcacgctccgtttgcttgtgatccgtcccgtgcacgctttctgtttgatcaaattccctggcgtgtttcaccatctgtgcttgacacgatgagttggttggtgttgtctttgcagCTTCGGGCGGCTCAGCTCAGGAGGATACTCTTGGAGCTTGGCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT