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

gtaagtgcaattttgtgttttctctgtagcattctaaagttctaccatgatagatgattgaaatcataacacctggatttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG

Basic information

species Zea mays
transcript GRMZM2G088088_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088088_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 6
gtaagtgcaattttgtgttttc--------tctgtagcattctaaagttcta---ccatgatagatgattgaaatcataacacctggatttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG
||||||||    || | | |||          ||    || || ||||   |    ||| | | ||  ||||| ||  |||  |||    || ||| |||||||||||||| || || |||||||||||| | ||||||||||||||||| || ||||||||||||||||||||||||
gtaagtgcctccttttctcttcatgtaacccttgcgctatgctgaagtctgaatttcataacaaattgttgaagtctgaactgctgttgcttaattcagGCATCCTTCGGCTTCAGTGCTCATTCCAGCTTTGCGCACGGTGGGTAACATCGTCACTGGGGATGACATGCAGACTCAG
















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|211452350|gb|FL292615.1|FL292615
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|6564217|gb|AW231839.1|AW231839
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|211452354|gb|FL292619.1|FL292619
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|213179381|gb|FM182985.1|FM182985
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCCGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|6587581|gb|AW244899.1|AW244899
EST:     CTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|211452351|gb|FL292616.1|FL292616
EST:     CAAGCTGNTATTGAATCTGGCGTGTTCCCTCGCCTTGNGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|211452349|gb|FL292614.1|FL292614
EST:     TGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: TGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|6865203|gb|AW360553.1|AW360553
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|211331752|gb|FL022649.1|FL022649
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTTCAGCTCTTCGCACGGTGGGTA-CAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT

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), 49 (downstream exon)
Score: 475

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 539

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 498

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 427

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaagttctaccatgatagatgattgaaatcataacacctggatttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG
                              tcataac  putative branch site (score: 427)
                                            tttttattt  putative PPT
                                        tggatttttattta  TA-rich tract