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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactgtgcattcattttttatacataaacattcgatctgcgatttgatgaactacttgggaacctcacgtctttgttcataactgcag

Basic information

species Zea mays
transcript GRMZM2G086805_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086805_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g43060.1 (Oryza sativa), 5'ss of exon 4
GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactgtgcattcattttttatacataaacattcgatctgcgatttgatgaactacttgggaacctcacg-tctttgttcataactgcag-----
| | |||||| |||||||||||||| || |||||| ||||||||||||| || ||||| ||||||  ||||  |    | |||| | |||  |    |||    | |  || | || | | || ||  |  |||   | | ||||| |   | |       
GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGGAGGAGTACCAAgtaggaacttagtgcac-ttttgtctacccatttgttc---tttcatttcggtgcatttctaggagatatcataatttgtgttccttcgttcgttccag
















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|7844125|gb|AW787328.1|AW787328
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|113686972|gb|DW842287.1|DW842287
EST:     CTGTCTCGGAGGAGCTTCCAGAAGAGTATCTAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTA
genomic: CTGTCTCGGAGGAGCTTCCAGAAGAGTATC-AAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTA
EST: gi|29129751|gb|CB380455.1|CB380455
EST:     CTGGG-GCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|32930934|gb|CF035746.1|CF035746
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGGGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|28986940|gb|CB351384.1|CB351384
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|211388869|gb|FL452911.1|FL452911
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|37378989|gb|CF626218.1|CF626218
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCTCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|4730597|gb|AI649763.1|AI649763
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|32943412|gb|CF048231.1|CF048231
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|26557678|gb|CA829913.1|CA829913
EST:     CTGGGTGCTATACCCTTGCTGTCTCGGGGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTTTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|37375940|gb|CF624458.1|CF624458
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|91869839|gb|EB400567.1|EB400567
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|45847108|gb|CN071051.1|CN071051
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|30087685|gb|CB885891.1|CB885891
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|93015254|gb|EB640774.1|EB640774
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|60339603|gb|DN206576.1|DN206576
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|211528033|gb|FL311002.1|FL311002
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|166410134|gb|EG136554.1|EG136554
EST:     TACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: TACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|60398153|gb|DN230969.1|DN230969
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|26557679|gb|CA829914.1|CA829914
EST:     CTGGG-GCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|60351934|gb|DN218907.1|DN218907
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|32857871|gb|CD997552.1|CD997552
EST:     CTGGGTGCTATACACTTGCTGGCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
EST: gi|7844126|gb|AW787329.1|AW787329
EST:     CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAA                         GGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA
genomic: CTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAA

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: 299

GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAAGTATCAAGACGGCAATGATGGTGTCTTGGTCCTGAAGCAGTATAGATAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAAGTATCAAGACGGCAATGATGGTGTCTTGGTCCTGAAGCAGTATAGATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAAGTATCAAGACGGCAATGATGGTGTCTTGGTCCTGAAGCAGTATAGATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 144

GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactg ... ataactgcagGGGATTTGTCAAGACAACAACGTGCAGTATGTGCCGCCCAAGCGTGTCTAAGTATCAAGACGGCAATGATGGTGTCTTGGTCCTGAAGCAGTATAGATAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGTTCATTCCTGGGTGCTATACACTTGCTGTCTCGGAGGAGCTTCCAGAAGAGTATCAAgtaaaaactgtgcattcattttttatacataaacattcgatctgcgatttgatgaactacttgggaacctcacgtctttgttcataactgcag

- - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - -  GAGCTT