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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcaatcatactgctctagcttcatatgcatcaaaaatactaaatgtttctctcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA

Basic information

species Zea mays
transcript GRMZM2G057158_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057158_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g03920.1 (Oryza sativa), 3'ss of exon 4
gtga-tcaatcatactgctctagcttcatatgcatcaaaaatacta-aatgtttctctcttttgca--gCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA
|| | | | | |||||||| |||  | ||    |||| |     ||  ||| || | |  | || |  ||||||||| |||||||||||||| ||||||||||||||||| ||||||||| |||| | 
gtaaattagttatactgctgtagtgt-atggaaatcagatggcttatgatgatttttttgtgtgtatagCAATTAATCTCATTCCAGCAGTCCTTGATGTCACAACTTGGTCAACAACAAGCTGGCCC
















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|26558010|gb|CA830245.1|CA830245
EST:     TTCAGAATCCAGAATTTCTTCGCCAGTTGACGTCTCCTGAAACATTGCAG                         CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
genomic: TTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
EST: gi|21828621|gb|BQ703305.1|BQ703305
EST:     TTCAGAATCCAGAATTTCTTCGCCAGTTGACGTCTCCTGAAACATTGCAG                         CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
genomic: TTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
EST: gi|67027074|gb|CO455823.1|CO455823
EST:     TTCAGAATCCAGAATTTCTTCGCCAGTTGACGTCTCCTGAAACATTGCAG                         CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
genomic: TTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
EST: gi|87156460|gb|DY401249.1|DY401249
EST:     TTCAGAATCCAGAATTTCTTCGCCAGTTGACGTCTCCTGAAACATTGCAG                         CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
genomic: TTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
EST: gi|113704257|gb|EE681761.1|EE681761
EST:     TTCAGAATCCAGAATTTCTTCGCCAGTTGACGTCTCCTGAAACATTGCAG                         CAATTAATTTCATTCCAGCAGTCTTTGATGTCACATCTTGGCCAACAACAA
genomic: TTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
EST: gi|78180947|gb|DV551320.1|DV551320
EST:     TTCAGAATCCAGAATTTCTTCGCCAGTTGACGTCTCCTGAAACATTGCAG                         CAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA
genomic: TTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAA

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: 224

TCCAAATGTACGTAACATGATGGAATCCAATACTCAAATGAGAGAAATGATTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

TCCAAATGTACGTAACATGATGGAATCCAATACTCAAATGAGAGAAATGATTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

TCCAAATGTACGTAACATGATGGAATCCAATACTCAAATGAGAGAAATGATTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 268

TCCAAATGTACGTAACATGATGGAATCCAATACTCAAATGAGAGAAATGATTCAGAATCCAGAATTTATTCGCCAGTTGACGTCTCCTGAAACATTGCAGgtgatcaatc ... tcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactgctctagcttcatatgcatcaaaaatactaaatgtttctctcttttgcagCAATTAATTTCATTCCAGCAGTCTTTGATGTCACAACTTGGCCAACAACAAACTGGACA
                              tactaaa  putative branch site (score: 268)
                                     tgtttctctcttttgc  CT-rich tract
                         aaaaatactaaatgtt  TA-rich tract