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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCCGCCGGAGTCCATTACTCCGCACTCCGTCTGGACGGCCAGGCTTCCGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatatatacttttgattgattgattgatgagtatggcgtagcctgttggccctgaatgcggcatgccctaatgtggtggttttgggcgcag

Basic information

species Zea mays
transcript GRMZM2G169462_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|78107197|gb|DV525615.1|DV525615
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211396287|gb|FK980044.1|FK980044
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|4609834|gb|AI600673.1|AI600673
EST:     GAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: GAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211393676|gb|FK980040.1|FK980040
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211393678|gb|FK980042.1|FK980042
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|71439100|gb|DR820150.1|DR820150
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211396286|gb|FK980043.1|FK980043
EST:     CGCAACGACGTCTGGCCTGGATAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|148987214|gb|EE031046.2|EE031046
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211393675|gb|FK980039.1|FK980039
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGWCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211396292|gb|FK980049.1|FK980049
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211396290|gb|FK980047.1|FK980047
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211396289|gb|FK980046.1|FK980046
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211396291|gb|FK980048.1|FK980048
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGTTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211393673|gb|FK980037.1|FK980037
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211396288|gb|FK980045.1|FK980045
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
EST: gi|211393674|gb|FK980038.1|FK980038
EST:     CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGARCCCTTTGTCATTG                         GTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA
genomic: CGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCA

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: 47 (upstream exon), 48 (downstream exon)
Score: 62

GCCGCCGCCGGAGTCCATTACTCCGCACTCCGTCTGGACGGCCAGGCTTCCGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 71

GCCGCCGCCGGAGTCCATTACTCCGCACTCCGTCTGGACGGCCAGGCTTCCGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 57

GCCGCCGCCGGAGTCCATTACTCCGCACTCCGTCTGGACGGCCAGGCTTCCGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

GCCGCCGCCGGAGTCCATTACTCCGCACTCCGTCTGGACGGCCAGGCTTCCGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatat ... ttgggcgcagGTGTTGCTGGGGGTGCATCGTCAGGCAAGAGTACCGTGTGCAAGATGATCATTGATCAGCTCCGTGACCAGCGTGTCGTGGTTGTTACGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCCGCCGGAGTCCATTACTCCGCACTCCGTCTGGACGGCCAGGCTTCCGCAACGACGTCTGGCCTGGAGAACGGCCACCAGGAGCCCTTTGTCATTGgttggtatatatacttttgattgattgattgatgagtatggcgtagcctgttggccctgaatgcggcatgccctaatgtggtggttttgggcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA