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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctccttcctcttagtgaaatacgtaccttgtggtacatcgagaaaaaatgtatgtcttcctatgttatgatcaacatcacctatatagcctata...

Basic information

species Zea mays
transcript GRMZM2G381933_T01
intron # 3
splice site 5'
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|50332159|gb|CO527285.1|CO527285
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|166510278|gb|EG235397.1|EG235397
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGC
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGC
EST: gi|4628225|gb|AI619099.1|AI619099
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|60359540|gb|DN226513.1|DN226513
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|60396268|gb|DN229137.1|DN229137
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|71767359|gb|DR965296.1|DR965296
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|60351624|gb|DN218597.1|DN218597
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|71756800|gb|DR954737.1|DR954737
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTTTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|60394781|gb|DN227651.1|DN227651
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|74242521|gb|DT650435.1|DT650435
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|37386793|gb|CF630585.1|CF630585
EST:     GCCATCAAAACC-TTTGTGTNCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: GCCATCAAAACCTTTTGTGT-CAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|211222854|gb|FL456564.1|FL456564
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|8665487|gb|BE186303.1|BE186303
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCCTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|60351898|gb|DN218871.1|DN218871
EST:     TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: TGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
EST: gi|211035729|gb|FL441186.1|FL441186
EST:     AAGCATCTCAGCACTACACTTTCAGAT                         GTTCAAATTGCNTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT
genomic: AAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTT

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), 48 (downstream exon)
Score: 92

ACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTTTACATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

ACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTTTACATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

ACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTTTACATAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 177

ACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctcc ... gcttgttcagGTTCAAATTGCTTCAGTCCTTGCAAAACTGTGCTTAGAGTTTTCTGATGTTTACATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTAGACACCGAGTGGGATTGTCTTCTAGGTACCCAGGAGAGTGGTCTAATGCCATCAAAACCTTTTGTGTCAAAGCATCTCAGCACTACACTTTCAGATgtatgtctccttcctcttagtgaaatacgtaccttgtggtacatcgagaaaaaatgtatgtcttcctatgttatgatcaacatcacctatatagcctata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaaa