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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCCAACCAACGCTGCTTTTTCCACCACTGCGACATGCTGAAGGAGTTGACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaatattttttctctcaaaaccattttaaagctttctaaagaagctacggatacgatgataattgacacttgtccagtgaaagtacagctaaaat...

Basic information

species Zea mays
transcript GRMZM5G844173_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os01g08700.3 (Oryza sativa), 5'ss of exon 11
TTCCCAACCAACGCTGCTTTTTCCACCACTGCGACATGCTGAAGGAGTTGACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaatattttttctctcaaaaccattttaaagctttctaaagaagctacggatacgatgataattgacacttgtccagtgaaagtaca-gctaaaat------
 |||||||| ||  | |||||||| |||||| ||||||| |||||||||||  | |||||||| ||||||||||||||||||||||| || || |  |||||||||| | |||  |        |||   ||    | |  |    |    | | || | ||  |  ||   |   ||    |  || || | ||||| |       
CTCCCAACCGACATTACTTTTTCCTCCACTGAGACATGCCGAAGGAGTTGAACTCCATCATGAGCCACTAGGTGGCTATGTATCATCGTACAAAAGGCAGgtatgcagtgtttcctgc------acctacttgctacctattctgtatttgatgtattcaatt-tcctttttatcagttttctcgaaatatatgctaataggcttgt
















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|32925707|gb|CF030519.1|CF030519
EST:     ACTTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAA                         TTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
genomic: ACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
EST: gi|32926485|gb|CF031297.1|CF031297
EST:     ACTTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAA                         TTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
genomic: ACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
EST: gi|32926778|gb|CF031590.1|CF031590
EST:     ACTTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAA                         TTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
genomic: ACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
EST: gi|32926028|gb|CF030840.1|CF030840
EST:     ACTTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAA                         TTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
genomic: ACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
EST: gi|32924657|gb|CF029469.1|CF029469
EST:     ACTTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAACCAA                         TTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
genomic: ACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
EST: gi|211118245|gb|FL244858.1|FL244858
EST:     ACGTACATCATGAACCACTAGGNGGCTATGTATCATCATATAAGAAACAG                         TTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT
genomic: ACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATT

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: 158

TTCCCAACCAACGCTGCTTTTTCCACCACTGCGACATGCTGAAGGAGTTGACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATTGCTTCTTTGTTGTGTGCTCATGGGCCTGATGTTGAGTGGAGAATATGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

TTCCCAACCAACGCTGCTTTTTCCACCACTGCGACATGCTGAAGGAGTTGACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATTGCTTCTTTGTTGTGTGCTCATGGGCCTGATGTTGAGTGGAGAATATGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

TTCCCAACCAACGCTGCTTTTTCCACCACTGCGACATGCTGAAGGAGTTGACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATTGCTTCTTTGTTGTGTGCTCATGGGCCTGATGTTGAGTGGAGAATATGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

TTCCCAACCAACGCTGCTTTTTCCACCACTGCGACATGCTGAAGGAGTTGACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaata ... ctaccggaagTTGGAAGTTCCTGCATCTGAGGCCACTATCGATGCCACTGCACAAGGCATTGCTTCTTTGTTGTGTGCTCATGGGCCTGATGTTGAGTGGAGAATATGTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCCAACCAACGCTGCTTTTTCCACCACTGCGACATGCTGAAGGAGTTGACGTACATCATGAACCACTAGGTGGCTATGTATCATCATATAAGAAACAGgtatgcaatattttttctctcaaaaccattttaaagctttctaaagaagctacggatacgatgataattgacacttgtccagtgaaagtacagctaaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaagaag