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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatattttttttgtcattagctttggtgtggtcacattgttcttcaagcagatggttccccttggggcatcaatcttgaattcttgatcgaaatatttggtttctttacctcag

Basic information

species Zea mays
transcript GRMZM2G058584_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058584_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 5'ss of exon 12
GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgta--ggcatattttttttgtcattagctttggtgtggtcacatt-gttcttcaagcagatggttccccttggggcatcaatcttgaattcttgatcgaaatatttggtttctttacctcag
|| || |||||||| ||| |||||||||||||||||||||||||||| |||||||||||||| |||||||||||  |  |||| || |||||||  ||||||  | |       |||   |||   ||  ||  ||  | ||||||     ||||   |   || | |||  | ||  ||    |                            
GCAATTTCATTCTCCAATATGTATGCCCCTGAGCATTTGATCATCAATGTAAAGGATGCTGAACAGTGGGAGGATCTTGTCGAGAATGCAGgtataggcatacctgtcagcgtcttaatcttgacctgaacattttcatacttcaa-----tggtaatctcaggcg-atcgttttttcatcacag----------------------------
















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|71309836|gb|DR791200.1|DR791200
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|22521319|gb|BU080130.1|BU080130
EST:     TGGGAAGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: TGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|22521320|gb|BU080131.1|BU080131
EST:     TCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: TCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|101389917|gb|EB816889.1|EB816889
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|78025141|gb|DV493528.1|DV493528
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAAGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|71432207|gb|DR813257.1|DR813257
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|76283948|gb|DV023516.1|DV023516
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|5081158|gb|AI738204.1|AI738204
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAAGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|76012898|gb|DT940068.1|DT940068
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|50325709|gb|CO520835.1|CO520835
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|211059003|gb|FL461767.1|FL461767
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|101394855|gb|EB819362.1|EB819362
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|71313988|gb|DR793606.1|DR793606
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|148957295|gb|EC903330.2|EC903330
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|78179432|gb|DV549805.1|DV549805
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAAGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|93017017|gb|EB642537.1|EB642537
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|86471200|gb|DY237570.1|DY237570
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|71432206|gb|DR813256.1|DR813256
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|71774595|gb|DR972473.1|DR972473
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|50331813|gb|CO526939.1|CO526939
EST:     CATCAACGTAAAGGATGCTGAGCAGGGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|14244763|gb|BG842701.2|BG842701
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|32840983|gb|CD980664.1|CD980664
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|101394357|gb|EB819113.1|EB819113
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
EST: gi|71769688|gb|DR967625.1|DR967625
EST:     CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAG                         GGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA
genomic: CATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGA

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

GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGAGCGGGACGAACCATGTCCTTCCGACCTATGGTTACGCAAGGATGTACAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 59

GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGAGCGGGACGAACCATGTCCTTCCGACCTATGGTTACGCAAGGATGTACAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 26

GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGAGCGGGACGAACCATGTCCTTCCGACCTATGGTTACGCAAGGATGTACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 33

GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatat ... tttacctcagGGTCAGTTTTCTTGGGCCAATGGACCCCAGAGAGCGTGGGCGATTATGCGAGCGGGACGAACCATGTCCTTCCGACCTATGGTTACGCAAGGATGTACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGATATCATTCTCAAATCTGTATGCCCCTGAGCATTTGATCATCAACGTAAAGGATGCTGAGCAGTGGGAGGAGTTCATCGAAAACGCAGgtaggcatattttttttgtcattagctttggtgtggtcacattgttcttcaagcagatggttccccttggggcatcaatcttgaattcttgatcgaaatatttggtttctttacctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG