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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtatccggatgccgtcaccgttactcacatttcttgttttagctttatatatgaagattttgatacagccatgtatatcatactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG

Basic information

species Zea mays
transcript GRMZM2G155437_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g01430.2 (Oryza sativa), 3'ss of exon 3
gtagtatccggatgccgtcaccgttactc-acatttct-tgttttagctttatat-----atgaagattttgatacagccatgtatatcatactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG
||||| |||  || |  |  |    |||  | | || |   |  |  ||   |||     ||      |||  |   ||||| |||  ||     ||||  | ||||||||||| || ||||||||||| || ||||||||||||| |||| |||| |||
gtagtctcctcatccaatggcttgcactttatacttatacatgatgactgcctatgcttgatatgagctttttttttgccatatattccact---gcagATTATTTCGAGAATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGCGACAGAAACG

upper sequence: GRMZM2G155437_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g01420.1 (Oryza sativa), 3'ss of exon 4
gtagtatccggatgccgtcaccgttactc-acatttct-tgttttagctttatatatgaagattttgatacagccatg---tatatcatactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG
||||| |||  || |  |  |    |||  | | || |   |  |  ||   |||     ||| |    |      ||   |||||   |||| |||  | ||||||||||| || ||||||||||| || ||||||||||||| || | |||| |||
gtagtctcctcatccaatggcttgcactttatacttatacatgatgactgcctatgctt-gatatgagcatttttttgccatatattccactg-cagATTATTTCGAGAATTCGAAGAGCATGATTTCGCCAGGACAGGAAGTATTGTGACAGAAACG
















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|18648715|gb|BM497534.1|BM497534
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|18450755|gb|BM429033.1|BM429033
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|211520197|gb|FL010166.1|FL010166
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAAATTTGAGGAGCATGATTT-GCAAGGACAGGAAGTACTG
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAA-TTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTG
EST: gi|211520200|gb|FL010169.1|FL010169
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCTAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|32907095|gb|CF011908.1|CF011908
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|15100390|gb|BI396181.1|BI396181
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|32838220|gb|CD977898.1|CD977898
EST:     GGCAACTAAGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTA
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTA
EST: gi|211520196|gb|FL010165.1|FL010165
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|211009194|gb|FL302295.1|FL302295
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|211520199|gb|FL010168.1|FL010168
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCTAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTTGCAAGGACAGGAAGTACTG
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTT-GCAAGGACAGGAAGTACTG
EST: gi|211520198|gb|FL010167.1|FL010167
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|78081476|gb|DV509888.1|DV509888
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|211011966|gb|FL302302.1|FL302302
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTT-GCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|78081475|gb|DV509887.1|DV509887
EST:     AAGGGATGATGTGGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: AAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
EST: gi|60394127|gb|DN226997.1|DN226997
EST:     GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAG                         GATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC
genomic: GGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGC

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: 130

TTCCTTCAAGGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

TTCCTTCAAGGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

TTCCTTCAAGGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 62

TTCCTTCAAGGCAACTCTGGTCTGTTATTCACCAATCTTCCAAGGGATGATGTTGAGAGgtagtatccg ... atactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttagctttatatatgaagattttgatacagccatgtatatcatactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG
                       ttttgat  putative branch site (score: 62)
         tttatatatgaagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtatccggatgccgtcaccgttactcacatttcttgttttagctttatatatgaagattttgatacagccatgtatatcatactggcagGATGTTTCGAGAATTTGAGGAGCATGATTTTGCAAGGACAGGAAGTACTGCGGCAGATACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT