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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaactaataatttgcctgtcttagtagtgtggccttttcatttatctgatgggaattgctacccttgtatagttaaacaacatcctctacaaaaaagttaaataactctgctgttggttggtctcaccttttgtggctgttgcgaaaacatactgcag

Basic information

species Zea mays
transcript GRMZM2G047894_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047894_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os03g18080.2 (Oryza sativa), 5'ss of exon 18
GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTG---TTGATTCTTCTTCGgtaattaac----taataatttgcctgtcttagtagtgtggccttttcatttatctgatgggaattgctacccttgtatagttaaacaacatcctctacaaaaaagttaaataactctgctgttggttggtctcaccttttgtggctgttgcgaaaacatactgcag
|||||||| |||||||| |||||||| |||||||||||| |||||| ||||||||||||||| |||||||   |||| ||| |  ||||||| | |    | ||  |||  ||| |||| || | | || | |||||||   |  |||| ||| |||   |||| |  ||  |                                                                                 
GATGCTCTAGACCTTATCAGCGGTTACTATACAGTCAGCAAAGGCATCTCTTCTCCTTTTCAAAATGGTGGATTTGAATCTGCAACGgtaatcagcattttcattttttttctgccttaataat-tagcatgttcatttcgatactggggattactaatattgtttgattgcag--------------------------------------------------------------------------------
















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|78021557|gb|DV489944.1|DV489944
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|71428422|gb|DR809472.1|DR809472
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|78022411|gb|DV490798.1|DV490798
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|32934739|gb|CF039551.1|CF039551
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTCGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|37387638|gb|CF631017.1|CF631017
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|5296286|gb|AI783056.1|AI783056
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCATTCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|37391643|gb|CF633065.1|CF633065
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTT-CTTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|31348859|gb|CD433216.1|CD433216
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|71325384|gb|DR799369.1|DR799369
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTTTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|18385140|gb|BM418339.1|BM418339
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|17970259|gb|BM277022.1|BM277022
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|24763373|gb|CA398549.1|CA398549
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|12968368|gb|BG265314.1|BG265314
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|113702249|gb|EE679753.1|EE679753
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
EST: gi|32850672|gb|CD990353.1|CD990353
EST:     TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCG                         TATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT
genomic: TCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACT

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), 49 (downstream exon)
Score: 75

GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaact ... catactgcagTATCTGCCGGTGGCTTCAGCAATCATAGTTGGTGGGATTACCGCGACAACTTTCACTCTCAGTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTCTTGACCTTATTAGCGGTTATTATACAGTCAGCCAAGGCAGCTCTTCTCCTTTTCATAATGGTGTTGATTCTTCTTCGgtaattaactaataatttgcctgtcttagtagtgtggccttttcatttatctgatgggaattgctacccttgtatagttaaacaacatcctctacaaaaaagttaaataactctgctgttggttggtctcaccttttgtggctgttgcgaaaacatactgcag

- - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - CAGCTC