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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatgtgggattatgctattgctagggaggagggactagggagctggtgatatttctttacgaaacatcatctgtttaatacctacaatgctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT

Basic information

species Zea mays
transcript GRMZM2G134889_T01
intron # 6
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|166429651|gb|EG299559.1|EG299559
EST:     ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAG                         GACTTCGCTGAAGGTTTCTTAGGAAGAC
genomic: ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTT-GGAAGAC
EST: gi|149077066|gb|EE165722.2|EE165722
EST:     ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAG                         GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
genomic: ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
EST: gi|71767590|gb|DR965527.1|DR965527
EST:     GATGGTGAGGTGTCACTTGAAGCTATAAAG                         GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
genomic: GATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
EST: gi|110965155|gb|EE185055.1|EE185055
EST:     GAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAG                         GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
genomic: GAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
EST: gi|31909789|gb|CD651094.1|CD651094
EST:     ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAGAG                         GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
genomic: ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
EST: gi|148938717|gb|EC883049.2|EC883049
EST:     AAGCTATAAAAG                         GACTTCGCTGAAGGTTTCTTGGAAAGACAAAGCTTACACCATTCTCCAAA
genomic: AAGCTAT-AAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGG-AAGAC-AAGCTTACACCATTCTACAAA
EST: gi|67020721|gb|CO449470.1|CO449470
EST:     ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAG                         GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
genomic: ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
EST: gi|32801735|gb|CD953971.1|CD953971
EST:     ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCGCTTGAAGCTATAAAG                         GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
genomic: ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
EST: gi|148974380|gb|EE025157.2|EE025157
EST:     GTGTCACTTGAAGCTATAAAG                         GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
genomic: GTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
EST: gi|78105578|gb|DV523996.1|DV523996
EST:     ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAG                         GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG
genomic: ATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCG

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: 277

GTTCTTGCTTACACTGGTAATGAAGATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 269

GTTCTTGCTTACACTGGTAATGAAGATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

GTTCTTGCTTACACTGGTAATGAAGATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 260

GTTCTTGCTTACACTGGTAATGAAGATGCTAGGAAATTTTTTCTTGATGGTGAGGTGTCACTTGAAGCTATAAAGgtaattgctg ... ctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgatatttctttacgaaacatcatctgtttaatacctacaatgctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT
                            gtttaat  putative branch site (score: 260)
                                           tgctctt  putative PPT
     tatttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatgtgggattatgctattgctagggaggagggactagggagctggtgatatttctttacgaaacatcatctgtttaatacctacaatgctcttgacagGACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
tgatgtg
- - - - - - - -ctattgc
- - - - - - - - - - - - - - - - - - - - - gctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctaca