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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtctttccttactcagaacttttgtcggttttctagtgttatttcgatccacaccattctgtagatgtagttcgagttttctagtgtcgattgatatctgacattggtagaggataactgggtttagaagtttacaaccctgtcgtctcctgatatgtttcttggttgtctcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCATATCTTCCACTGCAGCGCACATCAATGAGAGGAAAACCTGCAGAGTAGAC

Basic information

species Zea mays
transcript GRMZM2G094255_T01
intron # 7
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|76010862|gb|DT938032.1|DT938032
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|78027522|gb|DV495909.1|DV495909
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|31355338|gb|CD439695.1|CD439695
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|12970168|gb|BG266848.1|BG266848
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|78115024|gb|DV533412.1|DV533412
EST:     GACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: GACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|76284483|gb|DV024051.1|DV024051
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|47962518|gb|CN845227.1|CN845227
EST:     CAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|101397350|gb|EB820598.1|EB820598
EST:     CTTCGACAGGCAACAGAGTATGACTTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|94478728|gb|EB707686.1|EB707686
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|71327961|gb|DR800622.1|DR800622
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|60349510|gb|DN216483.1|DN216483
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|211377776|gb|FL432413.1|FL432413
EST:     GCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: GCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|74232835|gb|DT640749.1|DT640749
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|31664107|gb|CD573287.1|CD573287
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|78107717|gb|DV526135.1|DV526135
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCAT
EST: gi|78086465|gb|DV514858.1|DV514858
EST:     CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAG                         CTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAG
genomic: CTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAG

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: 18 (upstream exon), 32 (downstream exon)
Score: 2

AAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCATATCTTCCACTGCAGCGCACATCAATGAGAGGAAAACCTGCAGAGTAGAC


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 8

AAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCATATCTTCCACTGCAGCGCACATCAATGAGAGGAAAACCTGCAGAGTAGAC


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 6

AAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCATATCTTCCACTGCAGCGCACATCAATGAGAGGAAAACCTGCAGAGTAGAC


Block sizes: 21 (upstream exon), 49 (downstream exon)
Score: 2

AAAACTCACACCATATCATCGAGGCATCTTTCAAAGCGTTTGCTCGGGCCCTTCGACAGGCAACAGAGTATGACCTGCGCCGTCAAGGCACTGTCCCCAGgtctgtcttt ... tcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCATATCTTCCACTGCAGCGCACATCAATGAGAGGAAAACCTGCAGAGTAGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagtttacaaccctgtcgtctcctgatatgtttcttggttgtctcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCATATCTTCCACTGCAGCGCACATCAATGAGAGGAAAACCTGCAGAGTAGAC
                      tcctgat  putative branch site (score: 2)
                                        ttgtctc  putative PPT
                           atatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtctttccttactcagaacttttgtcggttttctagtgttatttcgatccacaccattctgtagatgtagttcgagttttctagtgtcgattgatatctgacattggtagaggataactgggtttagaagtttacaaccctgtcgtctcctgatatgtttcttggttgtctcaatggcagCTCCAAAGGTGTCTTGTCGAGATCATAGCATCGCAGTTTGGACGAACGCATATCTTCCACTGCAGCGCACATCAATGAGAGGAAAACCTGCAGAGTAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG