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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttcaagtctatgtgcccccttgtaatgcatgccttgaaacaagttcactgtaaagtggcagcatgatttcatcatttttttattcttgtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG

Basic information

species Zea mays
transcript GRMZM2G030144_T03
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030144_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 12
--agtttcaagtctatgtgcccccttgtaatgcatgccttgaaacaagttcactgtaaagtggca-gcatgatttcatcatttttttattcttgtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG
  |   ||  |   || |       |     || ||  |||  | |  |  |    ||  |||   ||||  | ||| |||  | |  || |  | ||| |||||||||||| ||||||||||| || |||||||||||||||||||||||| | || || || || ||||||||||  ||||||||||| || ||||| || 
tgatcctcttgcaaatattttaatataagtagcgtgatttgtgata--tctatctcaagatggtttgcattttgtcaccatactct-gttatcttattgccagGAGGATAAAGGAAATAGTTGCACAGAATAAAGGGAATACTGTGCTTGAACTACAACAGAGGTCAATTGAATTCAACTCCATTATACAGAGGCATCAGTCT

upper sequence: GRMZM2G030144_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA01G03890.1 (Glycine max), 3'ss of exon 12
agtttcaagtctatgtgcccccttgtaatgcatgccttgaaacaagttcactgtaaagt-ggcagcatgatttcatcatttttttattcttgtgttgt-----cagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG
      |    | ||   ||  |   | |  ||   ||    |   |    |||| | | | ||   |||  |     |||| || |  ||    | |      |||||||| ||||||||  |||  ||    |||||||    |||||| ||||||||||| ||| |||||||||||| ||| |||||   ||  ||||||   
------agacttgtgcaaccagtgcaagtttatttatttcctcttatattttgtatatttgacattttgacctggaagttttattctcttttgaatatggatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGAGCTATTGAATTCAATTCGATTATTGCAAAGCATCAAAAT

upper sequence: GRMZM2G030144_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 11
---agtttcaagtctatgtgcccccttgtaatgcatgccttgaaacaagttcactgtaaagtggcagcatgatttcatcatttttttattcttgtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG
    |  | |    | ||   ||  |   | |  ||   ||    |   |    |||| | |     | ||      | ||| | || |   | ||     |||||||| ||||||||  |||  ||    |||||||    |||||| ||||||||||| ||  |||||||||||||||| |||||   ||  ||||||   
ccatgcctaagacttgtgcaaccagtgcaagtttatttatttcctcttatat-ttgtatatt--tgacctggaaattttattctcttttgaatatgaatatagGAGGATCAAAGAAATTATTGTTCAGTTCAAAGGGAGCTTTGTGCTAGAATTGCAGCAGAGGGCTATTGAATTCAGTTCGATTATTTCAAAGCATCAAAAT

upper sequence: GRMZM2G030144_T03 (Zea mays), 3'ss of exon 11
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 12
-------agtttcaagtctatgtgcccccttgtaatgcatgccttgaaacaagttcactgtaaagtggcagcatgatttcatcatttttttattcttgtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG
        | || ||| |           || || |  |     |  | |      ||| |  | ||| |   |  ||| ||  || ||| | | ||   || | ||||||||||  || ||| |||  ||   |||||| |    |||||||||||||||||| ||||| |||||||| | |||||||||    |  ||||||   
cttagttgggttaaaggccgaacatatgattttactataatttcttcagc-----tactttttaatggaatttttttttaattgttctttaaatgtta-attat-agGAGGATAAGGGATATAATTGTCCAGTGTAAAGGAAGCCTTGTGCTTGAATTGCAGCAGAGATCCATTGAATTTAATTCCATTATTGGGAAGCATCAAAAT

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|71433260|gb|DR814310.1|DR814310
EST:     TGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGA                         GAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATT
genomic: TGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGAgtaagttatt ... gtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATT
EST: gi|211091952|gb|FL022378.1|FL022378
EST:     TGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGA                         GAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATT
genomic: TGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGAgtaagttatt ... gtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATT
EST: gi|166494311|gb|EG110655.1|EG110655
EST:     TGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGA                         GAGGATAAAAGAAATAGTTGCGC
genomic: TGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGAgtaagttatt ... gtgttgtcagGAGGATAAAAGAAATAGTTGCGC
EST: gi|67037313|gb|CO464163.1|CO464163
EST:     TGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGA                         GAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATT
genomic: TGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGAgtaagttatt ... gtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATT

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: 66

TAGAGGCTGCTCTTCAGCGCTACTCTGCAGATGTTACTACTAGGGCTATGTGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGAgtaagttatt ... gtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

TAGAGGCTGCTCTTCAGCGCTACTCTGCAGATGTTACTACTAGGGCTATGTGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGAgtaagttatt ... gtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

TAGAGGCTGCTCTTCAGCGCTACTCTGCAGATGTTACTACTAGGGCTATGTGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGAgtaagttatt ... gtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

TAGAGGCTGCTCTTCAGCGCTACTCTGCAGATGTTACTACTAGGGCTATGTGTCTTGTCTCTCTTTTGAAGCTTTCCTCCCGGTTTCCACCAACATCAGAgtaagttatt ... gtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcactgtaaagtggcagcatgatttcatcatttttttattcttgtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG
                                tttttttattcttgt  CT-rich tract
                    atgatttcatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttcaagtctatgtgcccccttgtaatgcatgccttgaaacaagttcactgtaaagtggcagcatgatttcatcatttttttattcttgtgttgtcagGAGGATAAAAGAAATAGTTGCGCAAAATAAAGGGAATACTGTGCTTGAATTGCAGCAAAGATCTATTGAATTCAGTTCCATTATACAAAGACATCAATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG