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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtacctaataactagacagacctgacctagtctctctctgtcgttattaatcttctaataaccgcatcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT

Basic information

species Zea mays
transcript GRMZM2G160430_T01
intron # 11
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|5296357|gb|AI783127.1|AI783127
EST:     GGCTCAAGAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG                         GTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
genomic: GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
EST: gi|32832825|gb|CD972503.1|CD972503
EST:     GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG                         GTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
genomic: GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
EST: gi|101387701|gb|EB815865.1|EB815865
EST:     GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG                         GTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
genomic: GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
EST: gi|37385615|gb|CF629958.1|CF629958
EST:     CTCATTGGAGCTATCTCG                         GTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
genomic: CTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
EST: gi|32927095|gb|CF031907.1|CF031907
EST:     GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG                         GTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
genomic: GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
EST: gi|148950293|gb|EC895852.2|EC895852
EST:     GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG                         GTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
genomic: GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
EST: gi|5846979|gb|AW000058.1|AW000058
EST:     GGCTCAAGAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCG                         GTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA
genomic: GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGA

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: 47 (upstream exon), 40 (downstream exon)
Score: 19

GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 212

GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 142

GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 84

GGCTCAACAACAGTAACCTGGACACGTGTCTCATTGGAGCTATCTCGgcaagtacct ... atcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgacctagtctctctctgtcgttattaatcttctaataaccgcatcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT
                                   taataac  putative branch site (score: 84)
                                              tcccatc  putative PPT
                       ttattaatcttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtacctaataactagacagacctgacctagtctctctctgtcgttattaatcttctaataaccgcatcccatcagGTTCTTGCCACTGGTGTCACAACCACGATCTTGGACAGAGCTGGCCGGAGAATCCTCCTCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC