Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCCCTCGTCCAAAACCCTAGCCCTCGCGCCGCCGCCGCCGTGCCCAGCGCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttatcctccgcgctgtaacatcgataggtggtgtttgtgggaatctagcgtctgatctgtgcccttttcgttgcttccag

Basic information

species Zea mays
transcript GRMZM5G851698_T02
intron # 1
splice site 5'
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|211068384|gb|FL392622.1|FL392622
EST:     GCTCGAGCTCCTCGCCTGCNGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|211542573|gb|FL410011.1|FL410011
EST:     GCTCGAGCTCCTCGCCTGCCGCGARCTCG-GCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|15312778|gb|BI478369.1|BI478369
EST:     GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|211431422|gb|FL393492.1|FL393492
EST:     GCTCGAGCTCCTCGCCTGCCGCGAGCTCG-GCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|20300566|gb|BQ163509.1|BQ163509
EST:     GCTCGCGCCGCAACGCCACCATGAAG                         -TCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGATGCTGGAAATCGAT
genomic: GCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|78079211|gb|DV507623.1|DV507623
EST:     CCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|5081006|gb|AI738268.1|AI738268
EST:     CTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|78024666|gb|DV493053.1|DV493053
EST:     CTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|29946749|gb|CB816306.1|CB816306
EST:     GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|19058404|gb|BM737071.1|BM737071
EST:     GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|21987949|gb|BQ779477.1|BQ779477
EST:     TGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: TGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|22819122|gb|BU499212.1|BU499212
EST:     CTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|15632345|gb|BI679438.1|BI679438
EST:     CCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|71428551|gb|DR809601.1|DR809601
EST:     GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|19057795|gb|BM736462.1|BM736462
EST:     TCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: TCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|20300275|gb|BQ163218.1|BQ163218
EST:     GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|31406383|gb|CD485115.1|CD485115
EST:     CCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         -TCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: CCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|31998590|gb|CD662145.1|CD662145
EST:     CAACGCCACCATGAAG                         -TCAACATCGCGAACCCG-CTACCGGGTGCCAGAA-AAGCTGGAAATCGAT
genomic: CAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
EST: gi|22935788|gb|BU572063.1|BU572063
EST:     GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAG                         TTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT
genomic: GCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGAT

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: 2767

TCCCCCTCGTCCAAAACCCTAGCCCTCGCGCCGCCGCCGCCGTGCCCAGCGCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1802

TCCCCCTCGTCCAAAACCCTAGCCCTCGCGCCGCCGCCGCCGTGCCCAGCGCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1547

TCCCCCTCGTCCAAAACCCTAGCCCTCGCGCCGCCGCCGCCGTGCCCAGCGCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1017

TCCCCCTCGTCCAAAACCCTAGCCCTCGCGCCGCCGCCGCCGTGCCCAGCGCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttat ... ttgcttccagTTCAACATCGCGAACCCGTCTACCGGGTGCCAGAAGAAGCTGGAAATCGATGACGACCAGAAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCCCTCGTCCAAAACCCTAGCCCTCGCGCCGCCGCCGCCGTGCCCAGCGCTCGAGCTCCTCGCCTGCCGCGAGCTCGCGCCGCAACGCCACCATGAAGgtaagcttatcctccgcgctgtaacatcgataggtggtgtttgtgggaatctagcgtctgatctgtgcccttttcgttgcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC