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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtaaaatgttgaaatgctagtccacaagttagggttttccctctcttttccgagtggacaaggcagataatcctgtgcattttttttatttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA

Basic information

species Zea mays
transcript GRMZM2G098815_T04
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098815_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g09610.1 (Oryza sativa), 3'ss of exon 10
tgtaaaatgttgaaatgctagtccacaagttagggttttccctctcttttccgagtggac--aaggcagataatcctgtgcattttttttatttgggt----gcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA
  |||   ||| |  | | || |    | |||   || |     |   | |    |  |   ||  |   || |  | |  |  |||| |   ||  |    |||||||||||||| ||||||||||||||||| ||||| ||||| || ||||||||||||||||||||||| || |||||||| ||||| || |||||||||  
--taactcgttta--ttccagcctc--atttatctttctttggttgcatgctatatttattgaaatcttttacttatttataagttttgtgcatgattctttgcagTTCAAGACCTCTTCATCGAGGTACAAGCTTTCTGCATTGAGTTCTCACGGATAAGGGAAGCAGCTGGCTTATTCCGGCTGCTCAAATCTTTGGAGTGA--

upper sequence: GRMZM2G098815_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv07s0130g00310.t01 (Vitis vinifera), 3'ss of exon 11
-tgtaaaatg-ttgaaatgctagtccacaagttagggttttccctctcttttccgagtggacaaggcagataatcctgtgcattttttttatttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA
     || || ||| |||   |    | | |  ||| |     |  | ||    || | |     || |||     | ||   |  || |  ||||||||||||||||| |||||||| || || ||||| |||||||| || || ||| |||| |||||||| |||||  | ||  |||| || ||  | ||||| |    
gcaccaagtgattggaattgcatggtatatgcaaggatgaatacaat-ttacaagaatagtttttgctgatt-ctttatgttatgattgtggttgggtgcagTTCAAGATCTTTTCATTGAAGTTCAAGCCTTCTGTATCGAGTTCTCAAGGATTAGGGAAGCTGCTGGACTATTTAGGCTTCTTAAAACTTTGGAATCTTG
















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|94474580|gb|EB703538.1|EB703538
EST:     AGTAGTTTGTGNNNNNNNGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|71759264|gb|DR957201.1|DR957201
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|71433708|gb|DR814758.1|DR814758
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|76014272|gb|DT941442.1|DT941442
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|211480513|gb|FL444430.1|FL444430
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|166427245|gb|EG305269.1|EG305269
EST:     TCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: TCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|110944532|gb|EE164689.1|EE164689
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|71449727|gb|DR830777.1|DR830777
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|84969904|gb|DW468307.1|DW468307
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|149082608|gb|EE171807.2|EE171807
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|148952744|gb|EC898725.2|EC898725
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|86472031|gb|DY238401.1|DY238401
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|60336775|gb|DN203748.1|DN203748
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
EST: gi|78022525|gb|DV490912.1|DV490912
EST:     ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACG                         TTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA
genomic: ACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGA

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), 49 (downstream exon)
Score: 78

GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

GATAAATACATGCAAAACAGACTTGTGAGACTAGTTTGTGTTTTTCTGCAGAGTCTTATCCGAAACAAGATTATAAACGgtgagtcact ... ttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttccgagtggacaaggcagataatcctgtgcattttttttatttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA
                                 cattttttttattt  CT-rich tract
                               tgcattttttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtaaaatgttgaaatgctagtccacaagttagggttttccctctcttttccgagtggacaaggcagataatcctgtgcattttttttatttgggtgcagTTCAAGACCTTTTCATCGAGGTACAAGCGTTCTGTATTGAATTTTCACGGATAAGGGAAGCAGCTGGTTTGTTCCGGCTACTCAAGTCGTTGGAGTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - -tgttgaa
- - - - - - - -tgctagt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcatt