Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctatattcctggtatgtttaagtgtatccttttttttggtttaagcaaatttaccacacactaatcaaaagattcaaaacgatcttttgtgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAGTGTTTAGATACGGGAGGTTTGTACCTCCTTGATGATGGCTTCACTTTCT

Basic information

species Zea mays
transcript GRMZM2G143725_T02
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|61118766|gb|DN559727.1|DN559727
EST:     TCAATTTTATCTATCCTTCTTTGTACAGAGTCGATGAAGTATNAACAATG                         GAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCA
genomic: TCAATTTTATCTATCCTTCTTTGTACAGAGTCGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCA
EST: gi|211056537|gb|FL371329.1|FL371329
EST:     CGATGAAGTATTAACAATG                         GAACCAAACAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
genomic: CGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
EST: gi|71445514|gb|DR826564.1|DR826564
EST:     TCAATTTTATCTATCCTTCTTTGTACAGAGTCGATGAAGTATTAACAATG                         GAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
genomic: TCAATTTTATCTATCCTTCTTTGTACAGAGTCGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
EST: gi|211478592|gb|FL369719.1|FL369719
EST:     CGATGAAGTATTAACAATG                         GAACCAAACAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
genomic: CGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
EST: gi|211424168|gb|FL418879.1|FL418879
EST:     CGATGAAGTATTAACAATG                         GAACCAAACAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
genomic: CGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
EST: gi|211169647|gb|FL398212.1|FL398212
EST:     CGATGAAGTATTAACAATG                         GAACCAAACAAGATTGATGGTTGGTTGAAACGCTTGGCATTAACGTTTCAG
genomic: CGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
EST: gi|211504702|gb|FL413778.1|FL413778
EST:     CGATGAAGTATTAACAATG                         GAACCAAACAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG
genomic: CGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAG

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: 48 (upstream exon), 45 (downstream exon)
Score: 87

ACGATGTGCTGCTGGTTTTAGCATGATGATATTGCCTGTAAAAAGGCTGCTCAATTTTATCTATCCTTCTTTGTACAGAGTCGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAGTGTTTAGATACGGGAGGTTTGTACCTCCTTGATGATGGCTTCACTTTCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 58

ACGATGTGCTGCTGGTTTTAGCATGATGATATTGCCTGTAAAAAGGCTGCTCAATTTTATCTATCCTTCTTTGTACAGAGTCGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAGTGTTTAGATACGGGAGGTTTGTACCTCCTTGATGATGGCTTCACTTTCT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 88

ACGATGTGCTGCTGGTTTTAGCATGATGATATTGCCTGTAAAAAGGCTGCTCAATTTTATCTATCCTTCTTTGTACAGAGTCGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAGTGTTTAGATACGGGAGGTTTGTACCTCCTTGATGATGGCTTCACTTTCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 132

ACGATGTGCTGCTGGTTTTAGCATGATGATATTGCCTGTAAAAAGGCTGCTCAATTTTATCTATCCTTCTTTGTACAGAGTCGATGAAGTATTAACAATGgtatgttgtt ... tgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAGTGTTTAGATACGGGAGGTTTGTACCTCCTTGATGATGGCTTCACTTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaatttaccacacactaatcaaaagattcaaaacgatcttttgtgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAGTGTTTAGATACGGGAGGTTTGTACCTCCTTGATGATGGCTTCACTTTCT
              cactaat  putative branch site (score: 132)
                                      tcttttgt  putative PPT
                 taatcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctatattcctggtatgtttaagtgtatccttttttttggtttaagcaaatttaccacacactaatcaaaagattcaaaacgatcttttgtgttttgcagGAACCAAATAAGATTGATGGTTGGTTGAAACGCTTGCCATTAACGTTTCAGTGTTTAGATACGGGAGGTTTGTACCTCCTTGATGATGGCTTCACTTTCT

- - - ttcctgg
- - - - - - - - - - - -tgtatcc
- - - - - - - - - - - - - - - - - ttttggt
- - - - - - - - - - - - - - - - - - - - - -aagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaacga