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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGAACGTGAGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatgaatcatgatgtactttgtaaacaatgtgaaggaggattaattattagtatgccatgatgtacttagtaaacaatgtaaaggagaattatt...

Basic information

species Zea mays
transcript GRMZM2G097226_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 10
ATAGAACGTGAGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatgaatcatgatgtactttgtaaacaatgtgaaggaggatta-attattagtatgccatgatgtacttagtaaacaatgtaaaggagaattatt-------
||||| |||||||||||||||||||| |||||||| | ||||||||||||||| |||||||| |||||  |||||         |||| || ||||||||| || | || || ||  |||     ||  | | || |  || |    ||   |    |    ||  |       
ATAGAGCGTGAGGGTAAAGATGTTACAATTACTGCATACTCCAAGATGGTTGGATATGCTCTTCAGgtgcgtcattt-------tgtaattggtaaacaatatggatgatgagtatgttacgtcgataactttatatgttttg-gctcatcatttgcgcagttttctatggtgt
















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|32802035|gb|CD954271.1|CD954271
EST:     AAGATGTTACCATTACTGCATTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|89754920|gb|DY685537.1|DY685537
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTGGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|78092463|gb|DV520837.1|DV520837
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|60394298|gb|DN227168.1|DN227168
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|211317947|gb|FL318710.1|FL318710
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|88757272|gb|DY541413.1|DY541413
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|76912074|gb|DV164558.1|DV164558
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGGTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|60343110|gb|DN210083.1|DN210083
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|211088145|gb|FL307530.1|FL307530
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAT
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|32829636|gb|CD969314.1|CD969314
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|86473456|gb|DY239826.1|DY239826
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|32829111|gb|CD968789.1|CD968789
EST:     AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG
EST: gi|211019433|gb|FL375798.1|FL375798
EST:     AAGATGTTACCATTACTGCATTCTCCAAGATGGTTGGCTATGCTCTCCAG                         GCTGCAGAGATACTGTCCAAGGAAGGAATCAGCGCTGAG
genomic: AAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG

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), 47 (downstream exon)
Score: 335

ATAGAACGTGAGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 457

ATAGAACGTGAGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 416

ATAGAACGTGAGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 715

ATAGAACGTGAGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatg ... ttgtcttcagGCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGAACGTGAGGGTAAAGATGTTACCATTACTGCGTTCTCCAAGATGGTTGGCTATGCTCTCCAGgtatgtcatgaatcatgatgtactttgtaaacaatgtgaaggaggattaattattagtatgccatgatgtacttagtaaacaatgtaaaggagaattatt

- - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggagaa