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

TGCCGCACCGCGCCGCCTCCAGACGCCTCGCTCGTCAGGTCTCTCCACCTCCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtctacggctctacgcgccagctcctcctccccctccccctccggccgagtcctcgtcgattttgggcgggcgcccctccgccggcggtctgtg...

Basic information

species Zea mays
transcript GRMZM2G078541_T01
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|148930587|gb|EE285247.2|EE285247
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|149071150|gb|EE159548.2|EE159548
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|149081109|gb|EE170213.2|EE170213
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|30087088|gb|CB885296.1|CB885296
EST:     GGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCG-CAGCAAGG-GG-CTCTCCAACCCTCCGGAGTCCGGAC
genomic: GGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|78118167|gb|DV536554.1|DV536554
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|149081984|gb|EE171150.2|EE171150
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|149014484|gb|EE044108.2|EE044108
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|211171921|gb|FK984131.1|FK984131
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAATCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|148949379|gb|EC894835.2|EC894835
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
EST: gi|71765670|gb|DR963607.1|DR963607
EST:     CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGG                         ATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC
genomic: CCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGAC

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: 38 (upstream exon), 49 (downstream exon)
Score: 38

TGCCGCACCGCGCCGCCTCCAGACGCCTCGCTCGTCAGGTCTCTCCACCTCCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGACCAGCAAG


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 35

TGCCGCACCGCGCCGCCTCCAGACGCCTCGCTCGTCAGGTCTCTCCACCTCCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGACCAGCAAG


Block sizes: 38 (upstream exon), 39 (downstream exon)
Score: 25

TGCCGCACCGCGCCGCCTCCAGACGCCTCGCTCGTCAGGTCTCTCCACCTCCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGACCAGCAAG


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 37

TGCCGCACCGCGCCGCCTCCAGACGCCTCGCTCGTCAGGTCTCTCCACCTCCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtct ... cttgctgcagATCTGCTGGAGCGCCAGCAAGGCGGTCTCTCCAACCCTCCGGAGTCCGGACCAGCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCGCACCGCGCCGCCTCCAGACGCCTCGCTCGTCAGGTCTCTCCACCTCCGCCTGCGAACGTTCGGCCCAGCTCCGGCGAGTTCCTCCGCAATTCCGGgtgagagtctacggctctacgcgccagctcctcctccccctccccctccggccgagtcctcgtcgattttgggcgggcgcccctccgccggcggtctgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccggc