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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactcatctggcatccaaaaggtagccatgaacatttcttagtgtgcctagtatgaaagtactgatattttctcctctggctttgtgcttgtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA

Basic information

species Zea mays
transcript GRMZM2G335287_T01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 27
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 26
aactcatctggcatccaaaaggtagccatgaac-atttcttagtgtgcctagtatgaaagtactgatattttctcctctggctttgtgcttgtttatcta-gGCCCCTGAT---GATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA
  |  | |     | ||   ||||   | | ||    |   | | |  | |   |     |  |  |  | | |  |     ||  || ||||| ||| | ||| ||||||   || | |||||||||  |||| || ||||| |  ||||||||||| ||||| ||||| |||||||| || || |||||||| |||||||   
--cataccatcattacacttggtactgaagtactgagtgggattttctccatagttggcttgtttttcatatgtatttaattttcctgtttgttgatcgaagGCACCTGATGCTGACGGGGCTGACAAAACTGACGATGAAGAGAATCCTATGATGGAGACTGTTAGGAGTAAATGTATCACTCAATTACTGCTACTTGGGG---
















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|32933407|gb|CF038219.1|CF038219
EST:     CCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAG                         GCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
genomic: CCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
EST: gi|21987959|gb|BQ779487.1|BQ779487
EST:     CCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAG                         GCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
genomic: CCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
EST: gi|32935168|gb|CF039980.1|CF039980
EST:     CCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAG                         GCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
genomic: CCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
EST: gi|78113830|gb|DV532219.1|DV532219
EST:     CCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAG                         GCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
genomic: CCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
EST: gi|6626560|gb|AW258092.1|AW258092
EST:     GTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAG                         GCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
genomic: GTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
EST: gi|32933086|gb|CF037898.1|CF037898
EST:     AAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAG                         GCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG
genomic: AAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATG

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: 48 (upstream exon), 49 (downstream exon)
Score: 399

AAGAATTATGGGCAATATGATGGATAATATTTTGGTCAGAAGTCTTACGTCCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 195

AAGAATTATGGGCAATATGATGGATAATATTTTGGTCAGAAGTCTTACGTCCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 145

AAGAATTATGGGCAATATGATGGATAATATTTTGGTCAGAAGTCTTACGTCCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 362

AAGAATTATGGGCAATATGATGGATAATATTTTGGTCAGAAGTCTTACGTCCAAATCAAAAGGTCGAACAGATGATATTGCTCCACCCTCACCTGTGAAGgtatatgtat ... gtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctagtatgaaagtactgatattttctcctctggctttgtgcttgtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA
              tactgat  putative branch site (score: 362)
                                          cttgttt  putative PPT
                 tgatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactcatctggcatccaaaaggtagccatgaacatttcttagtgtgcctagtatgaaagtactgatattttctcctctggctttgtgcttgtttatctagGCCCCTGATGATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - gcatcca
- - - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - - - - - - - tgcctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgat