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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAGCGGCGGAGGGGCTCGAGATTGCCAAGCTTGGGATCTCGTCCAAGATCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaagcgctggaatctttttaccttcatcaatcctgtctgaagctaccagagatcaagctgcccatatataatcataataacatgggaaaagtg...

Basic information

species Zea mays
transcript GRMZM2G107984_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|149061229|gb|EE157494.2|EE157494
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
EST: gi|211281261|gb|FL322092.1|FL322092
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCGGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
EST: gi|149089755|gb|EE179029.2|EE179029
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
EST: gi|211017399|gb|FL066295.1|FL066295
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCAACAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCGGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
EST: gi|14191124|gb|BG833354.1|BG833354
EST:     GCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCAGCAATGCAAGGCAAGGGACATGGTTGGCCGTGC
genomic: GCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGG-AAGGGACATGGTTGGCCGTGC
EST: gi|211017398|gb|FL066294.1|FL066294
EST:     TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAG                         AGAGCTGTCCTTGAGCCGGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC
genomic: TCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCC

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: 257

CGCAGCGGCGGAGGGGCTCGAGATTGCCAAGCTTGGGATCTCGTCCAAGATCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCCAAAACTGGGACTGGTAAAACTTTGGCATTTGGAATCCCCATAATGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

CGCAGCGGCGGAGGGGCTCGAGATTGCCAAGCTTGGGATCTCGTCCAAGATCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCCAAAACTGGGACTGGTAAAACTTTGGCATTTGGAATCCCCATAATGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

CGCAGCGGCGGAGGGGCTCGAGATTGCCAAGCTTGGGATCTCGTCCAAGATCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCCAAAACTGGGACTGGTAAAACTTTGGCATTTGGAATCCCCATAATGGATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 164

CGCAGCGGCGGAGGGGCTCGAGATTGCCAAGCTTGGGATCTCGTCCAAGATCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaa ... acctacacagAGAGCTGTCCTTGAGCCAGCAATGCAAGGAAGGGACATGGTTGGCCGTGCCAAAACTGGGACTGGTAAAACTTTGGCATTTGGAATCCCCATAATGGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAGCGGCGGAGGGGCTCGAGATTGCCAAGCTTGGGATCTCGTCCAAGATCGTCGAAAGGCTCGCCAGCAAGGGCATCACCAAGCTGTTCCCCATCCAGgtaacgagaagcgctggaatctttttaccttcatcaatcctgtctgaagctaccagagatcaagctgcccatatataatcataataacatgggaaaagtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT