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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatcattctttgtcattgaggttcatgtataatgggagattacctccatcccgtctgatatccttatatttgtcaacag

Basic information

species Zea mays
transcript GRMZM5G886883_T03
intron # 7
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|71305066|gb|DR788670.1|DR788670
EST:     GGAGGAGTCAAATATCCACTATCCTTCAAG                         CACTGATCCAGAAGCGGNTTGA-CTGACCTAC
genomic: GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGG-TTGAACTGACCTAC
EST: gi|78109684|gb|DV528100.1|DV528100
EST:     GGAGGAGTCAAATATCCACTATTCTTCAAG                         CACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACAT
genomic: GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACAT
EST: gi|93014964|gb|EB640484.1|EB640484
EST:     GGAGGAGTCCAATATCCACTATCCCTTCA-G                         CACTGATCCAGAAGCGGGTGAACTGACCTACTC
genomic: GGAGGAGTCAAATATCCACTATCC-TTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTC
EST: gi|148992844|gb|EE033671.2|EE033671
EST:     GGAGGAGTCAAATATCCACTATCCTTCAAG                         CACTGATCCAGAAGCGGTTGGACTGACCTACTCTGACATGAAATGTCT
genomic: GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACATGAAATGTCT
EST: gi|149088271|gb|EE177365.2|EE177365
EST:     GGAGGAGTCAAATATCCACTATCCTTCAAG                         CACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACATGAAATGTCTTGA
genomic: GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACATGAAATGTCTTGA
EST: gi|148996312|gb|EE035595.2|EE035595
EST:     GGAGGAGTCAAATATCCACTATCCTTCAAG                         CACTGATCCAGAAGCGGTTGAACTGACCTACTCT
genomic: GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCT
EST: gi|67031282|gb|CO460031.1|CO460031
EST:     GGAGGGAGTCAA-TATCCACTATCCTTTCA-G                         CACTGATCCAGAAGCGGGTGAACTGACCTACTCTGACAT
genomic: GGAGG-AGTCAAATATCCACTATCCTT-CAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACAT

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: 30 (upstream exon), 49 (downstream exon)
Score: 132

GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACATGAAATGTCTTGAACCA


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 132

GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACATGAAATGTCTTGAACCA


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 176

GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACATGAAATGTCTTGAACCA


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 110

GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatca ... ttgtcaacagCACTGATCCAGAAGCGGTTGAACTGACCTACTCTGACATGAAATGTCTTGAACCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGAGTCAAATATCCACTATCCTTCAAGgttggaatcattctttgtcattgaggttcatgtataatgggagattacctccatcccgtctgatatccttatatttgtcaacag

 GAGGAG