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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaattttgtgttttctctgtagcattctaaagttctaccatgatagatgattgaaatcataacacctggatttttatttag

Basic information

species Zea mays
transcript GRMZM2G088088_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088088_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 5'ss of exon 6
ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaattttgtgttttc--------tctgtagcattctaaagttcta---ccatgatagatgattgaaatcataacacctggatttttatttag
||||||||||||| || || || ||||||||||| ||||||||||| ||||||||||| || ||||| || ||||||||  | |||||||||||||| ||||||||||    || | | |||          ||    || || ||||   |    ||| | | ||  ||||| ||  |||  |||    || ||| ||
ATGCCTGCTGGGCTCTTTCTTATTTGTCTGATGGAACTAATGATAAGATCCAAGCTGTGATAGAATCAGGAGTGTTCCCAAGGCTTGTGGAACTTCTCATgtaagtgcctccttttctcttcatgtaacccttgcgctatgctgaagtctgaatttcataacaaattgttgaagtctgaactgctgttgcttaattcag

upper sequence: GRMZM2G088088_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S63_171V6.1 (Physcomitrella patens), 5'ss of exon 6
ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaattttgtgtt----ttctctgtagcattctaaagttctaccatgatagatgat-tgaaatcataacacctggatttttatttag--------
|||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| || ||||||||| | ||||||| |||||| |||||| | ||| || |||||| ||  | |    |     | |  |||     ||| | ||  |     | ||  |||  ||  |  | || || |   |  || ||           
ATGCATGCTGGGCTCTCTCTTACTTGTCCGATGGGACTAATGATAAGATCCAGGCGGTTATTGAAGCCGGCGTGTGCCCTCGTCTTGTGAACCTTTTGCTgtaagagctctctaacatcgcaatccattgttcatgtctcatgtgttgttcagttatgtgacgtgtgagtagaa-acttatgtagttgttcgatgtttcag

upper sequence: GRMZM2G088088_T01 (Zea mays), 5'ss of exon 6
lower sequence: PP1S63_171V6.2 (Physcomitrella patens), 5'ss of exon 6
ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaattttgtgtt----ttctctgtagcattctaaagttctaccatgatagatgat-tgaaatcataacacctggatttttatttag-----------
|||| |||||||| ||||| |||||||| ||||||||||||||||| ||||| || ||||||||| | ||||||| |||||| |||||| | ||| || |||||| ||  | |    |     | |  |||     ||| | ||  |     | ||  |||  ||  |  | || || |   |  || ||              
ATGCATGCTGGGCTCTCTCTTACTTGTCCGATGGGACTAATGATAAGATCCAGGCGGTTATTGAAGCCGGCGTGTGCCCTCGTCTTGTGAACCTTTTGCTgtaagagctctctaacatcgcaatccattgttcatgtctcatgtgttgttcagttatgtgacgtgtgagtagaa-acttatgtagttgttcgatgtttcagcag

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|211452350|gb|FL292615.1|FL292615
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|6564217|gb|AW231839.1|AW231839
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|211452354|gb|FL292619.1|FL292619
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|213179381|gb|FM182985.1|FM182985
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCCGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|6587581|gb|AW244899.1|AW244899
EST:     CTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|211452351|gb|FL292616.1|FL292616
EST:     CAAGCTGNTATTGAATCTGGCGTGTTCCCTCGCCTTGNGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|211452349|gb|FL292614.1|FL292614
EST:     TGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: TGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|6865203|gb|AW360553.1|AW360553
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT
EST: gi|211331752|gb|FL022649.1|FL022649
EST:     CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGAT                         GCATCCTTCGGCCTCTGTACTCATTTCAGCTCTTCGCACGGTGGGTA-CAT
genomic: CAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACAT

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: 475

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 539

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 498

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 427

ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaa ... ttttatttagGCATCCTTCGGCCTCTGTACTCATTCCAGCTCTTCGCACGGTGGGTAACATTGTAACTGGGGATGACATGCAGACTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCCTGCTGGGCGCTCTCATACTTGTCTGATGGGACTAATGATAAAATCCAAGCTGTTATTGAATCTGGCGTGTTCCCTCGCCTTGTGGAACTTCTGATgtaagtgcaattttgtgttttctctgtagcattctaaagttctaccatgatagatgattgaaatcataacacctggatttttatttag

- - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT