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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAATGCTGGTTTGGATAGCGCTGATTTGATCTCTCAGCTACGAGCTGAGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcacaaagacaagatgtttccattcttaacaaattatcttttacagaatctaatactagtcaaattgtgtggtccgcag

Basic information

species Zea mays
transcript EF517601.1_FGT012
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EF517601.1_FGT012 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 10
TGACAATGCTGGTTTGGATAGCGCTGATTTGATCTCTCAGCTACGAGCTGAGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcacaaa-gacaagatgtttccattcttaacaaattatcttttacagaatctaatactagtcaaattgtgtggtccgcag
||| ||||||||| |||| || |||||  ||||||||||||| ||||||||||||||||| ||||| | |||||||||||| ||||||||||||||||  ||||||| || ||  |  ||| |||   | | |      |  | |||  || |  | | | |||   ||     | || || ||||
TGATAATGCTGGTCTGGACAGTGCTGAGCTGATCTCTCAGCTCCGAGCTGAGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgacgaataatcagaagttcttagtttcttttga--accttagactgggtttgaaacttaacat----tatgatctgcag

upper sequence: EF517601.1_FGT012 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA12G09250.1 (Glycine max), 5'ss of exon 11
TGACAATGCTGGTTTGGATAGCGCTGATTTGATCTCTCAGCTACGAGCTGAGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcacaaagacaagatgtttccattc--ttaacaaattatcttttacagaatctaatactag---tcaaattgtgtggt-ccgcag---------
||| |||||||||||||| || ||||| ||||| |||||||| || || ||||| || || |||  ||  ||||||||||||||||| ||  | ||| ||||||||    |||       || ||  |||   || |   |  ||| |||    | |   | |   |   ||    ||| || |   ||           
TGATAATGCTGGTTTGGACAGTGCTGAGTTGATTTCTCAGCTCCGTGCAGAGCATCAGAAGGAGGGCTGTACTGCTGGAATTGATGTTATTTCTGGCTCTgtaagtattgaaactagtattggttgaatttatttgagttagcatcatttttgaattgccacatctggattctggatgtatgatattgccacatttcttt
















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|211264489|gb|FL417908.1|FL417908
EST:     AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAG
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAG
EST: gi|211238232|gb|FL378073.1|FL378073
EST:     AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GKTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAG
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAG
EST: gi|67015042|gb|CO443791.1|CO443791
EST:     AGCACCACATAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGGGGACATGCAANAGCTAGGGATTNCA-GAGTCGTTCAAGGTGA-GC
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGG-ACATGCAAAAGCTAGGGATT-CAAGAGTCGTTCAAGGTGAAGC
EST: gi|28931187|gb|CB334548.1|CB334548
EST:     AACACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGGGACATGCAAAAGCTAGGGATT
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATT
EST: gi|9952521|gb|BE639104.1|BE639104
EST:     AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGTGACATGCAAAAGTTGGGGATTCAAG
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAG
EST: gi|78110436|gb|DV528848.1|DV528848
EST:     AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGGGACATGCAAA
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAA
EST: gi|166411861|gb|EG176861.1|EG176861
EST:     AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGTGACATGCAAAAG
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAG
EST: gi|31364541|gb|CD448896.1|CD448896
EST:     AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGTGACATGCAAAAGTTGGGGATTCAAG
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAG
EST: gi|84976683|gb|DW475105.1|DW475105
EST:     AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGTGACATGCAAAAGTTGGGGATTCAAGAGTCGTTCAAGGTGAAGCAG
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAG
EST: gi|67010604|gb|CO439353.1|CO439353
EST:     AGCACCACANAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACT                         GTTGGGGACATGCAAAAGCTANGGATTCAAGAGTCGTTCAAGGTGAAGCAG
genomic: AGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAG

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: 404

TGACAATGCTGGTTTGGATAGCGCTGATTTGATCTCTCAGCTACGAGCTGAGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAGGCCATTCTTCTGTCTGCAACAGAGGCTGCCGAGATGATCCTCAGGGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 291

TGACAATGCTGGTTTGGATAGCGCTGATTTGATCTCTCAGCTACGAGCTGAGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAGGCCATTCTTCTGTCTGCAACAGAGGCTGCCGAGATGATCCTCAGGGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

TGACAATGCTGGTTTGGATAGCGCTGATTTGATCTCTCAGCTACGAGCTGAGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAGGCCATTCTTCTGTCTGCAACAGAGGCTGCCGAGATGATCCTCAGGGTCG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 175

TGACAATGCTGGTTTGGATAGCGCTGATTTGATCTCTCAGCTACGAGCTGAGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcac ... tggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAGGCCATTCTTCTGTCTGCAACAGAGGCTGCCGAGATGATCCTCAGGGTCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACAATGCTGGTTTGGATAGCGCTGATTTGATCTCTCAGCTACGAGCTGAGCACCACAAAGAGAACTCCACTGCTGGAATTGATGTCATCACAGGCACTgtaagttcacaaagacaagatgtttccattcttaacaaattatcttttacagaatctaatactagtcaaattgtgtggtccgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA