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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaactgaatctctgaaagaaaaatgttgaaatgttttttgagcttctgctgcgcagtttcagtttcttgcaccaaccaagctgtggtttcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG

Basic information

species Zea mays
transcript GRMZM2G076394_T01
intron # 13
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|78021364|gb|DV489751.1|DV489751
EST:     GGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAG                         GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
genomic: GGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAGgtaagtgccg ... tcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
EST: gi|6056529|gb|AW090919.1|AW090919
EST:     GGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAG                         GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
genomic: GGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAGgtaagtgccg ... tcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
EST: gi|166438226|gb|EG175816.1|EG175816
EST:     CAAAATTAACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAG                         GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
genomic: CAAAATT-ACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAGgtaagtgccg ... tcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
EST: gi|5929073|gb|AW056365.1|AW056365
EST:     GGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAG                         GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
genomic: GGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAGgtaagtgccg ... tcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
EST: gi|5525684|gb|AI861577.1|AI861577
EST:     GGCANAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAG                         GTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA
genomic: GGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAGgtaagtgccg ... tcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 23 (downstream exon)
Score: 2

TTGGCTTGGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAGgtaagtgccg ... tcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

TTGGCTTGGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAGgtaagtgccg ... tcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 219

TTGGCTTGGCAAAATTACAATGGAGAGTTATATTTCTCAGTTTCACATTTGGCTCAGgtaagtgccg ... tcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgctgcgcagtttcagtttcttgcaccaaccaagctgtggtttcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG
                                           tttcttttac  CT-rich tract
                                           tttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaactgaatctctgaaagaaaaatgttgaaatgttttttgagcttctgctgcgcagtttcagtttcttgcaccaaccaagctgtggtttcttttacagGTCTAGTATTCCGAACGGACAGCCAAAGTTGCTTCTATCTTTCTTACCAGATTATCCGATGCTTAACTTTTTGCTTACTACGACGATATTTCTGTCG

- - -ctgaatc
- - - - - - - - -aagaaaa
- - - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - -tgttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgtgg