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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTGCCGGTGGGAACTCATCGACAGAACCTTACATTGTTGTTCATAACATTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttcaatgaaatggaagaataaacaaataggaactattgcaaatacttgagtattagtaccaggatgcatgtctgtgactaaatgtacaaactgg...

Basic information

species Zea mays
transcript AC217401.3_FGT002
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217401.3_FGT002 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g49610.1 (Oryza sativa), 5'ss of exon 6
CACTGCCGGTGGGAACTCATCGACAGAACCTTACATTGTTGTTCATAACATTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttcaatgaaatggaagaataaacaaataggaactattgcaaatacttgagtattagtaccaggatgcatgtctgtgacta---aatgtacaaactgg
  ||||||||||||||||| | ||||| || || ||||||| |||||| ||  || |||||||||||||||||||||  |||||||| || || | |||||||||||    |   |   ||||||||| ||| || |||  ||  |   |||      ||  ||  |  |||    | | |  ||    ||     ||||   
TGCTGCCGGTGGGAACTCAGCAACAGAGCCATATATTGTTGCTCATAATATCATCTTATCTCATGCTACTGCAGTTGATAGATACCGTAACAAGTTCCAGgtattttct--ttctactaaagaataaagaaacagaaacagttagattgactctttcgttgttagtaacatggcaatttatatctcttcaacagttaaacca-
















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|32832647|gb|CD972325.1|CD972325
EST:     TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|67013218|gb|CO441967.1|CO441967
EST:     ATCTCATTCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: ATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|78075435|gb|DV503869.1|DV503869
EST:     CCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: CCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|149081710|gb|EE170863.2|EE170863
EST:     TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|149081712|gb|EE170865.2|EE170865
EST:     TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAC
genomic: TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|149013746|gb|EE043205.2|EE043205
EST:     TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|149014535|gb|EE044169.2|EE044169
EST:     TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|40336432|gb|CK370502.1|CK370502
EST:     TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|32834810|gb|CD974488.1|CD974488
EST:     TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
EST: gi|20507721|gb|BQ279747.1|BQ279747
EST:     TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAG                         GCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA
genomic: TTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAA

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: 216

CACTGCCGGTGGGAACTCATCGACAGAACCTTACATTGTTGTTCATAACATTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

CACTGCCGGTGGGAACTCATCGACAGAACCTTACATTGTTGTTCATAACATTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 39

CACTGCCGGTGGGAACTCATCGACAGAACCTTACATTGTTGTTCATAACATTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 113

CACTGCCGGTGGGAACTCATCGACAGAACCTTACATTGTTGTTCATAACATTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttca ... ttctcaatagGCAACTCAGAAAGGCAAGGTCGGGATAGTTCTTGACTTCAACTGGTATGAACCTTTTACAAACTCAACTGAAGATCAAAAAGCAGCGCAAAGGGCCAGGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACTGCCGGTGGGAACTCATCGACAGAACCTTACATTGTTGTTCATAACATTCTCCTATCTCATGCTACTGCAGTTGCAAGATACCGCAATAAATACCAGgtatttttcaatgaaatggaagaataaacaaataggaactattgcaaatacttgagtattagtaccaggatgcatgtctgtgactaaatgtacaaactgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaataa