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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgttatttctatttcatgttgacattattacacgggtttatcattgcttgtgggaactcttggaacatcattgattctaagtatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACTTGCAAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGAC

Basic information

species Zea mays
transcript GRMZM2G100913_T02
intron # 13
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|87156257|gb|DY401046.1|DY401046
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|31355723|gb|CD440080.1|CD440080
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|31909111|gb|CD650755.1|CD650755
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|67010842|gb|CO439591.1|CO439591
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|26559055|gb|CA831290.1|CA831290
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|211250422|gb|FL206023.1|FL206023
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|31364271|gb|CD448626.1|CD448626
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|29543802|gb|CB604182.1|CB604182
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|31363870|gb|CD448225.1|CD448225
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|211250423|gb|FL206024.1|FL206024
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
EST: gi|213179909|gb|FM186344.1|FM186344
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         NNNAGGCTGAGTCTGGTTTGGA
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGA
EST: gi|22549188|gb|BU101389.1|BU101389
EST:     CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAG                         GTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT
genomic: CTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACT

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), 48 (downstream exon)
Score: 303

ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACTTGCAAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 328

ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACTTGCAAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 430

ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACTTGCAAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 227

ATTATAGAATGCAGGCGAGTGTTGAAATGGACATATGCTTATGGCTACTATCTGGATGATAAGATCAAGAGTGAATTTTTTGAGTATCTGCAAGgttgttattt ... tatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACTTGCAAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatcattgcttgtgggaactcttggaacatcattgattctaagtatttgatagGTGAGGCTGAGTCTGGTTTGGAACGCCTGCATCAGTGCGCTGAGAAAGACTTGCAAATTTTTTTGCCGTCTGTGAAATCTGACAGCACTGAAACAACGAC
                                cattgat  putative branch site (score: 227)
                                         taagtattt  TA-rich tract