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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGGACGGCTATCCAGGAATTGCTACGCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcccccatcattatcagcactgtttcgtaacctatggtgtattcagatggatttcccccctcaaacatgcaggagatttgcatatcattttat...

Basic information

species Zea mays
transcript GRMZM5G870572_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G870572_T03 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os08g25060.1 (Oryza sativa), 5'ss of exon 17
CATTGGACGGCTATCCAGGAATTGCTACGCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc---cccatcattatcagcactgtttcgtaacctatg-gt-gtattcagatggatttcccccctcaaacatgcaggagatttgcatatcattttat
|| ||| | ||||||||||||||  | |  |||||||||||||| ||||||||||||| | |||| |||||||| |||||||||   |   ||||   || || ||||  || |||||  |||| || | |||  |||||   ||         | ||    | |  |  || || | |||  
CACTGGGCAGCTATCCAGGAATTATTGCAGCATTTTTGGTCATCATATCCAATAACAACTTCAGTTCTTTATAATAAGgtatattatcagtcccagacttttctgcaccattacgtaatttatgtgtagcatttggatggtaatcagtatcagtagattactggg--tcaca-ataaattt--
















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|31348758|gb|CD433115.1|CD433115
EST:     GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
EST: gi|166674440|gb|EG236190.1|EG236190
EST:     GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTA
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTA
EST: gi|29946463|gb|CB816162.1|CB816162
EST:     GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
EST: gi|71301572|gb|DR786840.1|DR786840
EST:     GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
EST: gi|89247122|gb|DY618908.1|DY618908
EST:     GCCATTTTTGGTCATTGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
EST: gi|74239224|gb|DT647138.1|DT647138
EST:     GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
EST: gi|24763305|gb|CA398481.1|CA398481
EST:     GCCATTTTTGGTCATGGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
EST: gi|148959669|gb|EE010942.2|EE010942
EST:     GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
EST: gi|4967176|gb|AI691877.1|AI691877
EST:     GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAG                         GTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG
genomic: GCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG

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: 44 (upstream exon), 49 (downstream exon)
Score: 102

CATTGGACGGCTATCCAGGAATTGCTACGCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 70

CATTGGACGGCTATCCAGGAATTGCTACGCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 76

CATTGGACGGCTATCCAGGAATTGCTACGCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 37

CATTGGACGGCTATCCAGGAATTGCTACGCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcc ... tgttttgaagGTTCAAAGAGTTAAAGAAGCTATGACACAGATATATCAAAAGCTGCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGGACGGCTATCCAGGAATTGCTACGCCATTTTTGGTCATCGTATCCAATAACAAGTGCAGTACTTTATAACAAGgtatatctcccccatcattatcagcactgtttcgtaacctatggtgtattcagatggatttcccccctcaaacatgcaggagatttgcatatcattttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccctc