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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaggttatatgtctaaggagacaattcagtgtgctgtttatgttctgttatgcataaaacaggaaaaatctcatgctcttttgtttttcattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC

Basic information

species Zea mays
transcript GRMZM2G097277_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097277_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 3'ss of exon 12
------attaggttatatgtctaaggagacaattcagtgtgctgtttatgttctgttatgcataaaacaggaaaaatctcatgctcttttgtttttcattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC
        |   | | ||   |    | | ||||   | | |  ||||| |  |||   |  |||  |||| | |  |||||  | | |  | ||||| || | ||| ||||||||||| || || || ||||||||| ||||||| |||||||||||| |  | |||||||||||||   | |||||||| || |||||||||||
tttagtcctctataagataatttgtaaaataatttcatctacc-tttatatcttgt---gggtaag-cagggagag-ctcatattatatgatctttcaattaacagGCAATTACCAAAAATTCTATTCCGCGATTAAAGCTGCCTATCCAGACATCAACGTCGTGTCAAGTTGTGATAAATCCACTATTTCTCCGTCCAACCCTGC
















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|67024258|gb|CO453007.1|CO453007
EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
EST: gi|211168064|gb|FL062250.1|FL062250
EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
EST: gi|67026679|gb|CO455428.1|CO455428
EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
EST: gi|71757747|gb|DR955684.1|DR955684
EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
EST: gi|5895641|gb|AW036887.1|AW036887
EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
EST: gi|67042721|gb|CO468976.1|CO468976
EST:     TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAG                         GAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA
genomic: TGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCA

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: 46 (upstream exon), 48 (downstream exon)
Score: 101

ACTTGGGGTTCTGTTCGTGCAGCAATGGGACACCCAGAACCCTTTAAGCTTGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 128

ACTTGGGGTTCTGTTCGTGCAGCAATGGGACACCCAGAACCCTTTAAGCTTGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 59

ACTTGGGGTTCTGTTCGTGCAGCAATGGGACACCCAGAACCCTTTAAGCTTGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 181

ACTTGGGGTTCTGTTCGTGCAGCAATGGGACACCCAGAACCCTTTAAGCTTGATTATGTTTCAATAGGAAATCAAGAATGTTGGATGCTCTACTATAGAGgttggcaaat ... cattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttatgcataaaacaggaaaaatctcatgctcttttgtttttcattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC
                         tctcatgctcttttgt  CT-rich tract
                                 tcttttgtttttcatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaggttatatgtctaaggagacaattcagtgtgctgtttatgttctgttatgcataaaacaggaaaaatctcatgctcttttgtttttcattttatagGAAATTACCAAAAGTTTTACTCAGCGATTAAATCTGCCTACCCAGACATCAACATTATATCAAGTTGTGATAGGCCAACTATTTCGCCATCCAACCCTGC

- - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - tgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - -atgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaaaa