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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACGGTTGGAGGTTACACGGACTTCTTTTGTTCTGTGCACCATGCAATGAATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttttctcggataatgtgctttgttggcatttaggggagcaaaagcagtatgttaatcagttgagatcagatcctgttgtctgaatattcttgc...

Basic information

species Zea mays
transcript GRMZM2G029566_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029566_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g10310.3 (Oryza sativa), 5'ss of exon 3
TCACGGTTGGAGGTTACACGGACTTCTTTTGTTCTGTGCACCATGCAATGAATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgta-tgtgttttctcggataatgtgctttgttggcatttaggggagcaaaagcagtatgttaatcagttgagatcagatcctgttgtctgaatattcttgc
||||||| ||||  ||||| |||||||||||||||||||||||||||| ||||||||| ||||||||||| ||||| ||||| |||||||| ||||||||||| ||| |||||| | |  |||   | || ||  | ||  |              ||    |  | |    |    ||  |  ||  | |  |       
TCACGGTAGGAGACTACACCGACTTCTTTTGTTCTGTGCACCATGCAAGGAATTGTGGGTTCATCTTCCGTGGGCCACAGACCCCAGTCAACCCAAATTGgtaatgtattttcttg-accatgccttgtgctgagacttgagacttgggttttgacataaacactaatctgcaatgtatgtt--tgcttcatcag------
















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|211126134|gb|FL125776.1|FL125776
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|71328229|gb|DR800748.1|DR800748
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|149044247|gb|EE047493.2|EE047493
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|149101399|gb|EE187518.2|EE187518
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148969714|gb|EE020586.2|EE020586
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|32851376|gb|CD991057.1|CD991057
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|211277944|gb|FK998813.1|FK998813
EST:     AATTGTGGATTCATCTTCCGAGGGCCGSAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTAT
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTAT
EST: gi|60348819|gb|DN215792.1|DN215792
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148990772|gb|EE032185.2|EE032185
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148932701|gb|EC876670.2|EC876670
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148940815|gb|EC885642.2|EC885642
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148964333|gb|EC905725.2|EC905725
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|78124353|gb|DV542737.1|DV542737
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148956082|gb|EC901838.2|EC901838
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148955041|gb|EC900548.2|EC900548
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTTTTAGTTGTGT
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTAT-AGTTGTGT
EST: gi|148983240|gb|EE029206.2|EE029206
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|149076833|gb|EE165488.2|EE165488
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|149042087|gb|EE047065.2|EE047065
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148949167|gb|EC894603.2|EC894603
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|71421618|gb|DR805518.1|DR805518
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148941367|gb|EC886277.2|EC886277
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148959990|gb|EE153229.2|EE153229
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|76920587|gb|DV168250.1|DV168250
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCTAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|149009361|gb|EE041411.2|EE041411
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|148946154|gb|EC891448.2|EC891448
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
EST: gi|211272507|gb|FK998769.1|FK998769
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTTATCTTCCAGTAGGATACAATTGGGCGAGCATCATCTATAGTTGTG
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTT-ATCTTCCAGTAGGATACAAT-GGGCGAGCATCATCTATAGTTGTG
EST: gi|89764162|gb|DY691069.1|DY691069
EST:     AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTG                         GTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC
genomic: AATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTC

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: 439

TCACGGTTGGAGGTTACACGGACTTCTTTTGTTCTGTGCACCATGCAATGAATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 601

TCACGGTTGGAGGTTACACGGACTTCTTTTGTTCTGTGCACCATGCAATGAATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 395

TCACGGTTGGAGGTTACACGGACTTCTTTTGTTCTGTGCACCATGCAATGAATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 3327

TCACGGTTGGAGGTTACACGGACTTCTTTTGTTCTGTGCACCATGCAATGAATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttt ... gtcaattcagGTTTTATCTTCCAGTAGGATACAATGGGCGAGCATCATCTATAGTTGTGTCTGGAACCAATGTCATTAGGCCCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACGGTTGGAGGTTACACGGACTTCTTTTGTTCTGTGCACCATGCAATGAATTGTGGATTCATCTTCCGAGGGCCGCAGACTCCAGTCAATCCAAATTGgtatgtgttttctcggataatgtgctttgttggcatttaggggagcaaaagcagtatgttaatcagttgagatcagatcctgttgtctgaatattcttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagcag