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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTATTTCTGCTGCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttacactaattttattaaatgcaagtaagaataaacaaatgttagccgttaaaacatcaatttgtttccaaacttgttatgtgcataacctagc...

Basic information

species Zea mays
transcript GRMZM2G048804_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048804_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g07100.1 (Oryza sativa), 5'ss of exon 5
GAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTATTTCTGCTGCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttacactaattttattaaatgcaagtaa--------gaataaacaaatgttagccgttaaaacatcaa---tttgtttccaaacttgttatgtgcataacctagc
||||||| |||||||| || |||||  ||||||| |||||||||||||| || ||||||||  | |||||||| ||||||||| ||| |||||| |||||||| | ||  |||||||||  | ||| |||||||        ||| ||  |||| |    | |  || ||||||   | |   || |||| ||  |  |            
GAGATGATTATGATGACGACGGGCAGAAATTATCCGAAGCTATTTCTGCAGCAAAAGTGCGTTCTGAGAGTTGTTCATCATTCCTGAGAGCTGCTATCAGgtaaggttgtactaattttcattaatccaagtaaattgagtagaaaaactaaatatccttcatgcaagcatcaaacatcttcatctaaacatggcagttt-----------
















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|33771157|gb|CF272818.1|CF272818
EST:     GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAG                         GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
genomic: GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
EST: gi|71773197|gb|DR971110.1|DR971110
EST:     GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAG                         GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
genomic: GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
EST: gi|33467112|gb|CF244161.1|CF244161
EST:     GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAG                         GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
genomic: GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
EST: gi|6056483|gb|AW090873.1|AW090873
EST:     GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAG                         GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTC
genomic: GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTC
EST: gi|50339822|gb|CO534948.1|CO534948
EST:     GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAG                         GTGGTCTGCTGAGTTTGGAACATC
genomic: GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATC
EST: gi|31349428|gb|CD433785.1|CD433785
EST:     GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAG                         GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
genomic: GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
EST: gi|32850448|gb|CD990129.1|CD990129
EST:     GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAG                         GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
genomic: GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
EST: gi|74236761|gb|DT644675.1|DT644675
EST:     GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAG                         GTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT
genomic: GCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGT

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), 43 (downstream exon)
Score: 114

GAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTATTTCTGCTGCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 174

GAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTATTTCTGCTGCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 127

GAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTATTTCTGCTGCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 205

GAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTATTTCTGCTGCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttac ... atgttttgagGTGGTCTGCTGAGTTTGGAACATCAAGAAATGGTTCTTCTGAGCTTCACGTTATGTTAGCAGAATACATATATTCGGAATCTCCAGAGACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGATGACTATGATGATGAGGGGCATCAATTATCTGAAGCTATTTCTGCTGCCAAAGTGCGGGCAGAGAGTTGCTCATCATTCATGAAAGCTGCAATCAGgtaggtttacactaattttattaaatgcaagtaagaataaacaaatgttagccgttaaaacatcaatttgtttccaaacttgttatgtgcataacctagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaataa