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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCAGAGAGATCCCGCGCCTCTACACCGAGCAGCAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaacaacagccggtccacagagatactacccttaatcttgcttacatcaaacacagtctcactttaaaaactttgctcaaggagcaaaagggtaa...

Basic information

species Zea mays
transcript GRMZM2G065494_T01
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065494_T01 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os02g04710.1 (Oryza sativa), 5'ss of exon 17
GCCCAGAGAGATCCCGCGCCTCTACACCGAGCAGCAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaacaacagccggtccacagagatactacccttaatcttgcttacatcaaacacagtctcactttaaaaactttgctcaaggagcaaaagggtaa---
||  ||||||||||    ||| | || |||||||| ||||||||||||||||| || || || || || |||||||||||||||||||||   ||   ||   |||  |    |  ||    ||  |||||   |  ||| | |||    | || |   |       ||  | |    ||  |    
GCTGAGAGAGATCCAATTCCTTTGCATCGAGCAGCGAAGGTTTTGATCAACTTACAATCGGAAGATGGTGAATTTCCCCAGCAAgtaagttctaat--ccatcccatgggttcatgacatgaaacgttgctc-tagaaaagaaagtgatgcatttacttcagcctgtaataatcttgtggtgattca
















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|60400796|gb|DN233603.1|DN233603
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|488246|gb|T18827.1|T18827
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GATATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACCCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|32838148|gb|CD977826.1|CD977826
EST:     CAAGGGTTTTGATAAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGTAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGT
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGT
EST: gi|17352566|gb|BM173680.1|BM173680
EST:     CAAGGGTTTTGATAAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCA-                         GAGATCATAGGAGTGTTCAACAAGA-CTGCATGATCAGTTACTCCCAGT-C
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|32839382|gb|CD979063.1|CD979063
EST:     CAAGGGTTTTGATAAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGTAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGT
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGT
EST: gi|31357306|gb|CD441663.1|CD441663
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAAAAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|18179995|gb|BM381205.1|BM381205
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|31357419|gb|CD441776.1|CD441776
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTAAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|211195144|gb|FL314128.1|FL314128
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|110952656|gb|EE172708.1|EE172708
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|33094833|gb|CF054827.1|CF054827
EST:     CAAGGGTTTTGATAAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|149084840|gb|EE174345.2|EE174345
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|211125929|gb|FL443336.1|FL443336
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
EST: gi|12967988|gb|BG264935.1|BG264935
EST:     CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAA                         GAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC
genomic: CAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTAC

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: 124

GCCCAGAGAGATCCCGCGCCTCTACACCGAGCAGCAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTACAGGAACACCTTCCCGATCTGGGCTCTGGGAGAGTACCGGTGCCGAGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

GCCCAGAGAGATCCCGCGCCTCTACACCGAGCAGCAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTACAGGAACACCTTCCCGATCTGGGCTCTGGGAGAGTACCGGTGCCGAGTCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 117

GCCCAGAGAGATCCCGCGCCTCTACACCGAGCAGCAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTACAGGAACACCTTCCCGATCTGGGCTCTGGGAGAGTACCGGTGCCGAGTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GCCCAGAGAGATCCCGCGCCTCTACACCGAGCAGCAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaaca ... cccaacgcagGAGATCATAGGAGTGTTCAACAAGAACTGCATGATCAGTTACTCCCAGTACAGGAACACCTTCCCGATCTGGGCTCTGGGAGAGTACCGGTGCCGAGTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCAGAGAGATCCCGCGCCTCTACACCGAGCAGCAAAGGTTTTGATCAACTTGCAGTCAGAGGACGGAGAATTTCCCCAGCAAgtaagtaacaacagccggtccacagagatactacccttaatcttgcttacatcaaacacagtctcactttaaaaactttgctcaaggagcaaaagggtaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagcaaaa