Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctcattttattctacttgcacgccttctataaatagctgcaatcaaaaaaattgcaggattagcatcacgagcttcaatattttcatatttgccatgttgttatgtcactgagtttttctctgcactctttgttag

Basic information

species Zea mays
transcript GRMZM2G057056_T01
intron # 4
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|28911394|gb|BM351713.2|BM351713
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|28911370|gb|BM340835.2|BM340835
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|28985527|gb|CB350686.1|CB350686
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|28911294|gb|BM351042.2|BM351042
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|31664474|gb|CD573407.1|CD573407
EST:     GATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|37401613|gb|CF638174.1|CF638174
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|211433116|gb|FL461630.1|FL461630
EST:     GTTTATTTCCMCGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|28911464|gb|BM349702.2|BM349702
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|28911286|gb|BM339599.2|BM339599
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|28911265|gb|BM350764.2|BM350764
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
EST: gi|88752936|gb|DY537077.1|DY537077
EST:     GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTG                         ATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT
genomic: GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACAT

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: 45 (upstream exon), 47 (downstream exon)
Score: 59

GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 77

GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 47

GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 25

GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctc ... tctttgttagATCGATGAGGGAGTAGTATTTAGGGTCGCAGGTGGTTTGCTGCTTGAACATCCATTGACGCTGCCGTTTGTCGAAGCAGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATTTCCACGATATACCAGATGAGGTCATCAAGAGCTTGgtatgttctcattttattctacttgcacgccttctataaatagctgcaatcaaaaaaattgcaggattagcatcacgagcttcaatattttcatatttgccatgttgttatgtcactgagtttttctctgcactctttgttag

- - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - -  GAGCTT