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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttataacttatatctgcttatctggtaccaaattagcaatcacattccataactgtcagcttatggtggcaatgctacaacttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG

Basic information

species Zea mays
transcript GRMZM2G160430_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160430_T04 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 9
---------gtaagtttataacttatatc-tgcttatctg--gtaccaaat-tagcaatcacattccataactgtcagcttatggtggcaatgctacaacttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG
          ||| ||||||| |  |||  | ||| | ||   |||||||| |||  |  | |||  |||| ||  |   ||           ||   |  |   ||||||||||||||||||||||||  ||||||||||||||||||| ||| | ||| | |||||| ||||||||||||||||||| ||||
gtaatttccttaactttataattggtattgtacttttatgccataccaaatatagggactaaattttataattggaattgta-----------cttttaactgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
















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|5296357|gb|AI783127.1|AI783127
EST:     CAGTAAGCTTTCAAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATT                         CTAGGAATCGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
genomic: CAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
EST: gi|148950294|gb|EC895853.2|EC895853
EST:     CAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATT                         CTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
genomic: CAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
EST: gi|32832825|gb|CD972503.1|CD972503
EST:     CAGTAAGCTTTCAAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATT                         CTAGGAATCGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
genomic: CAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
EST: gi|32927095|gb|CF031907.1|CF031907
EST:     CAGTAAGCTTTCAAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATT                         CTAGGAATCGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
genomic: CAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
EST: gi|148950293|gb|EC895852.2|EC895852
EST:     CCAAAAGAAATACCGCACGCCTCTAATT                         CTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
genomic: CCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
EST: gi|5846979|gb|AW000058.1|AW000058
EST:     CAGTAAGCTTTCAAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATT                         CTAGGAATCGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA
genomic: CAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATA

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: 32 (upstream exon), 32 (downstream exon)
Score: 9

ATAGCTGTAGCATCAGCAAACAAAAGTGGTACAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 184

ATAGCTGTAGCATCAGCAAACAAAAGTGGTACAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 93

ATAGCTGTAGCATCAGCAAACAAAAGTGGTACAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 73

ATAGCTGTAGCATCAGCAAACAAAAGTGGTACAATAAGCTTTCGAGAGTTGAACCAAAAGAAATACCGCACGCCTCTAATTgtaagtttat ... cttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatcacattccataactgtcagcttatggtggcaatgctacaacttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG
           ccataac  putative branch site (score: 73)
                                             cttcccgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttataacttatatctgcttatctggtaccaaattagcaatcacattccataactgtcagcttatggtggcaatgctacaacttcccgcagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAATTGTATAATCTTTTATTCAGGTAGCATCTTCAAAGCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG