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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCAGCTACTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattttgtttctttacctgacggacataacctatcagttgtcattgtcttggttgagtatttaaagctattataatctgcag

Basic information

species Zea mays
transcript GRMZM2G159295_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159295_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 5'ss of exon 6
CCCAACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCAGCTACTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattttgtttctttacctgacggacataacctatcagttgtcattgtcttggttgagtatttaaagctattataatctgcag
||| |||||||||||||||||||||||||||||||||||||||||  | ||| | ||||||||||| ||||||||||||||||||||||||||| ||||||| | |  ||||||| | | | | ||          | ||  |||||||| ||| | |    || | |||| |  |  ||| |||||
CCCGACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCCCCAACTATACATGGAAATGAAAATGATGTTGAAGAGCTAGAGATGTTGTTGGAGgtcttt--tttgtttttctgcatcacaa--------tgtc--ttgtcattctctggctgagatactaaaagtttcttaaatttgcag

upper sequence: GRMZM2G159295_T01 (Zea mays), 5'ss of exon 6
lower sequence: AT5G64560.1 (Arabidopsis thaliana), 5'ss of exon 7
CCCAACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCAGCTACTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgt--attttgt------ttctttacctgacggacataacctatcagttgtc--attgtcttggttgagtatttaaagctattataa-tctgcag
|||||| || || || || || ||||||||||| ||||| |||  ||| || || |||||  ||||||||||||||||||| || || ||||| || |||||||||  ||  ||       |  |||| ||||      | | |||||     |   | || |  |    | ||   |   || | |||  | | |||
CCCAACAATAGGCTCTAAGATTTCAAGAGCAAGTAGAGCGAGTTTAGCCACAGTTCATGGGGATGAGAATGATGTTGAAGAACTTGAAATGTTACTCGAGgtttgttgatcctgcacaaaatcttttatctgat---tctgatctatcttccattcaaatgccaagtccaaatacacacgtct-tgatatctttacag
















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|149107574|gb|EE189456.2|EE189456
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|148945148|gb|EC890346.2|EC890346
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|149105622|gb|EE291166.2|EE291166
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|149102719|gb|EE188266.2|EE188266
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|29544199|gb|CB604579.1|CB604579
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|149107640|gb|EE189521.2|EE189521
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|211094045|gb|FL457288.1|FL457288
EST:     ATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: ATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|60337564|gb|DN204537.1|DN204537
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|37382291|gb|CF628086.1|CF628086
EST:     CTGTGCATGAAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|149073143|gb|EE161419.2|EE161419
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|14203648|gb|BG837325.1|BG837325
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|76291165|gb|DV030733.1|DV030733
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
EST: gi|14243174|gb|BG840819.2|BG840819
EST:     CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAG                         GCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG
genomic: CTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG

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: 231

CCCAACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCAGCTACTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 459

CCCAACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCAGCTACTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 442

CCCAACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCAGCTACTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 516

CCCAACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCAGCTACTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattt ... taatctgcagGCATATTTCATGCAAGTTGATGGCACATTAAACAAATTGACAACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAACTATTGGTTCAAAAATATCAAGAGCAAGCAGAGCCAGTGCAGCTACTGTGCATGGAAATGAGAATGATGTTGAAGAGCTAGAGATGTTGCTGGAGgtttgtattttgtttctttacctgacggacataacctatcagttgtcattgtcttggttgagtatttaaagctattataatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA