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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctcgtccaaaagttcaatgtcaaggtatcaggtacactggtcaattactgtttttgacactgtttgttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATATCTA

Basic information

species Zea mays
transcript GRMZM2G307906_T01
intron # 8
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|76290809|gb|DV030377.1|DV030377
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|211458274|gb|FL247609.1|FL247609
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATAC-ANGGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTTCTTACT
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAG-TACAGAGATTGATAAATCAGCGAACAAATTCTTCT-CTTACT
EST: gi|211458279|gb|FL247614.1|FL247614
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|18175729|gb|BM350937.1|BM350937
EST:     ATTATTGCATTCAAG                         ATGCCAAGTACAGAGATTGATAGATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|211458288|gb|FL247623.1|FL247623
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGA
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGA
EST: gi|74241997|gb|DT649911.1|DT649911
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|211294858|gb|FL410176.1|FL410176
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|211298410|gb|FL370609.1|FL370609
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|78091777|gb|DV520151.1|DV520151
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|5268368|gb|AI770332.1|AI770332
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACT
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACT
EST: gi|211397249|gb|FL247600.1|FL247600
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCCAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|78091778|gb|DV520152.1|DV520152
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|74241998|gb|DT649912.1|DT649912
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|74236877|gb|DT644791.1|DT644791
EST:     ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAG                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
genomic: ATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGG
EST: gi|211458286|gb|FL247621.1|FL247621
EST:     TCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTTCA-G                         ATACCCAGTACCGAGATTGATAAATCA
genomic: TCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATT-CAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCA
EST: gi|211397257|gb|FL247608.1|FL247608
EST:     CAGTACCTACTTTTTGCTGCAGAGCCCTATGNNAATTAT-GCATTTCA-G                         ATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTG
genomic: CAGTACCTACTTTTTGCTGCAGAGCCCTATGA-AATTATTGCATT-CAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTG

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), 47 (downstream exon)
Score: 140

AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATATCTA


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 103

AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATATCTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 162

AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATATCTA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 84

AAAGTCCAAAGTTGGGATAAGGGTTATCAGTACCTACTTTTTGCTGCAGAGCCCTATGAAATTATTGCATTCAAGgtaatctcgt ... gttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATATCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaggtatcaggtacactggtcaattactgtttttgacactgtttgttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATATCTA
                               ttttgac  putative branch site (score: 84)
                    tcaatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctcgtccaaaagttcaatgtcaaggtatcaggtacactggtcaattactgtttttgacactgtttgttgctgcagATACCAAGTACAGAGATTGATAAATCAGCGAACAAATTCTTCTCTTACTGGGATCCTGACAAGAAGGAATATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA