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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGGTTGGAGCAAATATGGTCAGCTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatataccttgtacaaacattccgtgacatggtttcaagaacttcattttcgctttgctaggatttagaaagatgatggttccatacttccatgcac...

Basic information

species Zea mays
transcript GRMZM2G003565_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G003565_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g35570.3 (Oryza sativa), 5'ss of exon 5
TTATGGTTGGAGCAAATATGGTCAGCTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatacc--ttgtacaaacattccgtgacatggtttcaagaacttcattttcgctttgctaggatt-tagaaagatgatggttccatacttcca----tgcac---------------------------------
|||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| |||| || || || |||||| ||||||| |||||| |    |      ||  || |||| | ||  |    | |||  |||    |      |   | |||| |    | ||  | |  |  | ||        | |||                                 
TTATGGTTGGAGCAAATATGGTCAACTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAACTAGAGGCCTTAAAGGATAGCTCTATATCGCAGgtacactcgctagcactaacaatattctgggaactatgctgaagttcttggcctgtttcctctgatgattgtcagtatatatttgcccttttctcttggaatttcacacgtcttatttacaaagtattctactaatttag

upper sequence: GRMZM2G003565_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv07s0031g02560.t01 (Vitis vinifera), 5'ss of exon 6
TTATGGTTGGAGCAAATATGGTCAGCTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatataccttgtacaaacattccgtgacatggtttcaagaacttcattt--tcgctttgctaggatttagaaagatgatggttccatacttccat-gcac-----
 ||||| ||||||||||||||||||||||| |||||||||||||| |||||  |   ||| |||||| | ||||| ||| | || |     || ||  ||||     |  ||| |||    |||   |||  ||  || |    ||||||||  ||   |||     | |  | || || |  |||   |      || | |      
ATATGGGTGGAGCAAATATGGTCAGCTAGGACATGGTGATTTTGAGGATCACCTCACTCCTCATAAACTGGAAGCCTTGCAGGAAAATTTGATTTCTGAGgt-----tctcttttactcctatt---tgaattgtgttgattttcttcatttattcaggttgaagataatatggaatattaatgttttgtgtgggaatagtatttgtg
















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|29130842|gb|CB381546.1|CB381546
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|211087172|gb|FL255715.1|FL255715
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|194716840|gb|FK933999.1|FK933999
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCACACGATGGCACTTACATCAGAGGGAGAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|211471127|gb|FL255671.1|FL255671
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
EST: gi|211476174|gb|FL255694.1|FL255694
EST:     ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAG                         ATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT
genomic: ATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTT

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), 49 (downstream exon)
Score: 622

TTATGGTTGGAGCAAATATGGTCAGCTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTTTACGGATGGGGATGGAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 588

TTATGGTTGGAGCAAATATGGTCAGCTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTTTACGGATGGGGATGGAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

TTATGGTTGGAGCAAATATGGTCAGCTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTTTACGGATGGGGATGGAACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 901

TTATGGTTGGAGCAAATATGGTCAGCTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatatac ... tgtgatttagATTTCAGGCGGCTGGAGGCATACGATGGCACTTACATCAGAGGGAAAGCTTTACGGATGGGGATGGAACAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGGTTGGAGCAAATATGGTCAGCTAGGGCATGGTGATTTTGAAGATCATTTAGTTCCACATAAAGTAGAAGCTTTGAAAGATAGCACTATATCCCAGgtaaatataccttgtacaaacattccgtgacatggtttcaagaacttcattttcgctttgctaggatttagaaagatgatggttccatacttccatgcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC