Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttgaggtttattatcttttaacctttatgatcatattccttcaattagtgtatgatctgatcattttttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCATTGAGGGCATTGGACAGCACTGTCCCGCATGGGTGCTGTGAACCAAGAA

Basic information

species Zea mays
transcript GRMZM2G041842_T01
intron # 1
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|78081856|gb|DV510268.1|DV510268
EST:     CATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGG                         TCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCA
genomic: CATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGGgtatgatttg ... tttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCA
EST: gi|148936551|gb|EC880669.2|EC880669
EST:     CATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGG                         TCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCA
genomic: CATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGGgtatgatttg ... tttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCA
EST: gi|101394859|gb|EB819364.1|EB819364
EST:     CATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGG                         TCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCA
genomic: CATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGGgtatgatttg ... tttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCA

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), 41 (downstream exon)
Score: 72

AACTGAGATTGCTGTAAATAATATAGAACATTCCTGTTTTCCTCCAGAAACATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGGgtatgatttg ... tttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCATTGAGGGCATTGGACAGCACTGTCCCGCATGGGTGCTGTGAACCAAGAA


Block sizes: 43 (upstream exon), 39 (downstream exon)
Score: 36

AACTGAGATTGCTGTAAATAATATAGAACATTCCTGTTTTCCTCCAGAAACATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGGgtatgatttg ... tttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCATTGAGGGCATTGGACAGCACTGTCCCGCATGGGTGCTGTGAACCAAGAA


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 72

AACTGAGATTGCTGTAAATAATATAGAACATTCCTGTTTTCCTCCAGAAACATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGGgtatgatttg ... tttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCATTGAGGGCATTGGACAGCACTGTCCCGCATGGGTGCTGTGAACCAAGAA


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 94

AACTGAGATTGCTGTAAATAATATAGAACATTCCTGTTTTCCTCCAGAAACATCTGCTGCTGATTTGCCAGCAGATGAAGGCTCCGAGCAGGCTTCCTGGgtatgatttg ... tttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCATTGAGGGCATTGGACAGCACTGTCCCGCATGGGTGCTGTGAACCAAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttatgatcatattccttcaattagtgtatgatctgatcattttttttctcagTCAAAATGTCCAGAGCAATCAGAGGAATTGTTAGGGTTGATTGTTAATTCATTGAGGGCATTGGACAGCACTGTCCCGCATGGGTGCTGTGAACCAAGAA
                                 atctgat  putative branch site (score: 94)
                                       tcattttttttctc  CT-rich tract
                                    tgatcatttttttt  TA-rich tract