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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgacatttcgattctcttctattctgttccggcagtgctgtgccaatgaagtcttgaactgttatctctgataaactcagatgtcctagttcatcgttcatcgctaaccatagggcaactaacgttccttgcag

Basic information

species Zea mays
transcript GRMZM2G077669_T01
intron # 7
splice site 5'
intron type U2

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|50336618|gb|CO531744.1|CO531744
EST:     CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|24769648|gb|CA404777.1|CA404777
EST:     CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAATCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|91872557|gb|EB402514.1|EB402514
EST:     CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|60344176|gb|DN211149.1|DN211149
EST:     CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|149030376|gb|EE154822.2|EE154822
EST:     CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTA                         AAGCCCAAGAAATGATCGGGGAAGATGAGCCCCTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|6095300|gb|AW119967.1|AW119967
EST:     TCGGATCTACACAAATCATCAACTA                         AGGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: TCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|149009313|gb|EE153898.2|EE153898
EST:     CTTGCAGAGACGGCTGATGGTTGTTTTGGATTTACACAAGTCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|18964118|gb|BM660820.1|BM660820
EST:     CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACATAAGTCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|211446928|gb|FL456344.1|FL456344
EST:     CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|211399039|gb|FL440973.1|FL440973
EST:     CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAATCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
EST: gi|91872556|gb|EB402513.1|EB402513
EST:     CTTGCAGAGACGGGTGATGGTTGTCTCGGATCTACACAAGTCATCAACTA                         AAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA
genomic: CTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGA

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: 47 (upstream exon), 46 (downstream exon)
Score: 67

ATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGACAGAACCATACGTGCAAATCAGATACGAAGGCGGCATACACAGAGCAAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 99

ATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGACAGAACCATACGTGCAAATCAGATACGAAGGCGGCATACACAGAGCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 259

ATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGACAGAACCATACGTGCAAATCAGATACGAAGGCGGCATACACAGAGCAAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 153

ATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgaca ... ttccttgcagAAGCACAAGAAATGATCGGGGAAGATGAGCCACTAAATCCTTAGACGTCGACAGAACCATACGTGCAAATCAGATACGAAGGCGGCATACACAGAGCAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTACACAAGTCATCAACTAgtatgtgacatttcgattctcttctattctgttccggcagtgctgtgccaatgaagtcttgaactgttatctctgataaactcagatgtcctagttcatcgttcatcgctaaccatagggcaactaacgttccttgcag

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