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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGCAGGCGGAGGCGATCACCTCCGCCATCACGGAGGTCCTCAACGACAGCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcctcgcctttggcattgcgtggatggttgtttcatagaggtttgcttgggtcctgtggacggattgctcggttgtctttctcatttggtggtcttggtactctgtttgcag

Basic information

species Zea mays
transcript GRMZM2G116427_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116427_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g49890.1 (Oryza sativa), 5'ss of exon 2
CAAGCAGGCGGAGGCGATCACCTCCGCCATCACGGAGGTCCTCAACGACAGCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaa-gcgcctcgcctttggcattgcgtggatggttgtttcatagaggtttgcttgggtcctgtggacggattgctcggttgtctttctcatttggtggtcttggtactctgtttgcag
 |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||   |    ||| | |  |   || | |  |||         ||||||      | || |    || | | | ||  ||||  |||   |                       
GAAGCAGGCGGAGGCGATCACCTCCGCGATCACGGAGGTCCTCAACGACAGCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgtaacgccattttttttttggaccgtacggctag--gtt--------atttgctccca--cggttggttaatgggtggttttgcttttccatgcag-----------------------
















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|21330027|gb|BQ485408.1|BQ485408
EST:     GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
EST: gi|21330705|gb|BQ486086.1|BQ486086
EST:     GCCTCGAGAGCATCTCCGAGTCCTTCGGCTCCAAGGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGA
genomic: GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGA
EST: gi|32869175|gb|CF008857.1|CF008857
EST:     GGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: GGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
EST: gi|21390595|gb|BQ528644.1|BQ528644
EST:     GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
EST: gi|21480787|gb|BQ577470.1|BQ577470
EST:     GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
EST: gi|26455505|gb|CA827088.1|CA827088
EST:     GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
EST: gi|22546799|gb|BU099110.1|BU099110
EST:     TCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: TCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
EST: gi|21481481|gb|BQ578164.1|BQ578164
EST:     GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
EST: gi|87154790|gb|DY399579.1|DY399579
EST:     GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: GCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
EST: gi|32906186|gb|CF010999.1|CF010999
EST:     GGCCGAGATGCAGAAG                         AGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG
genomic: GGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAG

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: 43 (upstream exon), 49 (downstream exon)
Score: 31

CAAGCAGGCGGAGGCGATCACCTCCGCCATCACGGAGGTCCTCAACGACAGCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 50

CAAGCAGGCGGAGGCGATCACCTCCGCCATCACGGAGGTCCTCAACGACAGCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 40

CAAGCAGGCGGAGGCGATCACCTCCGCCATCACGGAGGTCCTCAACGACAGCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 37

CAAGCAGGCGGAGGCGATCACCTCCGCCATCACGGAGGTCCTCAACGACAGCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcct ... ctgtttgcagAGTGAGATGCTGCAGGAGTCCAATATCTCCAAGTTCAAGTCCCAAGTGCAGAGCTCGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGCAGGCGGAGGCGATCACCTCCGCCATCACGGAGGTCCTCAACGACAGCCTCGAGAGCATCTCCGAGTCCTTCGTCTCCAAGGCCGAGATGCAGAAGgcaagcgcctcgcctttggcattgcgtggatggttgtttcatagaggtttgcttgggtcctgtggacggattgctcggttgtctttctcatttggtggtcttggtactctgtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG