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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGCTGCGAGTACGGAGCGCTCGTTTTCGGGCTTCCTGCATGCGATATCACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcgcctgcctcagatctcgcagcctagccaggttcttggcctgggaactcttgcttgtgagcgtgccctagatctgctagctgctggccctgc...

Basic information

species Zea mays
transcript GRMZM2G118063_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|50335761|gb|CO530887.1|CO530887
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|78087580|gb|DV515973.1|DV515973
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|149100689|gb|EE186778.2|EE186778
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|50323259|gb|CO518385.1|CO518385
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|37421574|gb|CF648487.1|CF648487
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|71767000|gb|DR964937.1|DR964937
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|71299781|gb|DR785898.1|DR785898
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|149102846|gb|EE288187.2|EE288187
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACCGGCCGGGATCGGAG                         AATGAAAGCTGACGATATCGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|149102070|gb|EE287534.2|EE287534
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|149015319|gb|EE045135.2|EE045135
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|50328875|gb|CO524001.1|CO524001
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|148953688|gb|EC899049.2|EC899049
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
EST: gi|148934302|gb|EC878328.2|EC878328
EST:     CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAG                         AATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA
genomic: CACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 386

GCCAGCTGCGAGTACGGAGCGCTCGTTTTCGGGCTTCCTGCATGCGATATCACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTAGCTGGGACCGTACGTACCGTGCTGCCATTGTTCATGACTCCGGCAAGGC


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 43

GCCAGCTGCGAGTACGGAGCGCTCGTTTTCGGGCTTCCTGCATGCGATATCACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTAGCTGGGACCGTACGTACCGTGCTGCCATTGTTCATGACTCCGGCAAGGC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 127

GCCAGCTGCGAGTACGGAGCGCTCGTTTTCGGGCTTCCTGCATGCGATATCACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcg ... ttttttgcagAATGAAAGCTGACGATATAGAGCAAGATGAGCTAGGGTTCGCGAGGCACTAGCTGGGACCGTACGTACCGTGCTGCCATTGTTCATGACTCCGGCAAGGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAGCTGCGAGTACGGAGCGCTCGTTTTCGGGCTTCCTGCATGCGATATCACCGACGAAACGTGTCTCTGGAAGAAGGCATCACAGGCCGGGATCGGAGgtacagatcgcctgcctcagatctcgcagcctagccaggttcttggcctgggaactcttgcttgtgagcgtgccctagatctgctagctgctggccctgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG