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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgccttcgctcgccccgccgattggccccctgattctgtcctgtctgcgtggattcatgcgattgacgcggggttttctcttgttctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTCTTTGGTTCCTCGCCCCAGGATGTGGAGTGATAGCCGAGGAGGCTTCCGT

Basic information

species Zea mays
transcript GRMZM2G172001_T04
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|50339560|gb|CO534686.1|CO534686
EST:     CCGCGACTACAAAGGCCGCCGCGCCGGCATGATCAAGGCCCTCACCACTG                         ATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTC
genomic: CCGCGACTACAAAGGCCGCCGCGCCGGCATGATCAAGGCCCTCACCACTGgtacgccttc ... tctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTC
EST: gi|71303373|gb|DR787790.1|DR787790
EST:     CCGCGACTACAAAGGCCGCCGCGCCGGCATGATCAAGGCCCTCACCACTG                         ATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTC
genomic: CCGCGACTACAAAGGCCGCCGCGCCGGCATGATCAAGGCCCTCACCACTGgtacgccttc ... tctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTC

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), 43 (downstream exon)
Score: 334

GGGGGCTCTGGGCTGGCGCCCAACGCCGCGCACACCGCGGACGAGGTCTTCCGCGACTACAAAGGCCGCCGCGCCGGCATGATCAAGGCCCTCACCACTGgtacgccttc ... tctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTCTTTGGTTCCTCGCCCCAGGATGTGGAGTGATAGCCGAGGAGGCTTCCGT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 42

GGGGGCTCTGGGCTGGCGCCCAACGCCGCGCACACCGCGGACGAGGTCTTCCGCGACTACAAAGGCCGCCGCGCCGGCATGATCAAGGCCCTCACCACTGgtacgccttc ... tctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTCTTTGGTTCCTCGCCCCAGGATGTGGAGTGATAGCCGAGGAGGCTTCCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 65

GGGGGCTCTGGGCTGGCGCCCAACGCCGCGCACACCGCGGACGAGGTCTTCCGCGACTACAAAGGCCGCCGCGCCGGCATGATCAAGGCCCTCACCACTGgtacgccttc ... tctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTCTTTGGTTCCTCGCCCCAGGATGTGGAGTGATAGCCGAGGAGGCTTCCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GGGGGCTCTGGGCTGGCGCCCAACGCCGCGCACACCGCGGACGAGGTCTTCCGCGACTACAAAGGCCGCCGCGCCGGCATGATCAAGGCCCTCACCACTGgtacgccttc ... tctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTCTTTGGTTCCTCGCCCCAGGATGTGGAGTGATAGCCGAGGAGGCTTCCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtctgcgtggattcatgcgattgacgcggggttttctcttgttctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTCTTTGGTTCCTCGCCCCAGGATGTGGAGTGATAGCCGAGGAGGCTTCCGT
                     gattgac  putative branch site (score: 125)
                                  ttttctcttgttctgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgccttcgctcgccccgccgattggccccctgattctgtcctgtctgcgtggattcatgcgattgacgcggggttttctcttgttctgtgcaagATGTGGAGAGGTTCTTCAAACTCTGTGACCCTGGTGAGTGCGCTCGATCTCTTTGGTTCCTCGCCCCAGGATGTGGAGTGATAGCCGAGGAGGCTTCCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG