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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACTTGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttcttggaccgtctggccaaatttgtgtcctgcggtcgcgatcccagatcccatattgattccgttttttgctgttggtttcttggttgtcctacag

Basic information

species Zea mays
transcript GRMZM2G003692_T07
intron # 2
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|211527525|gb|FL409928.1|FL409928
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|211174932|gb|FL421412.1|FL421412
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCKK-AGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|149101270|gb|EE187382.2|EE187382
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|211280391|gb|FL376816.1|FL376816
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|211267130|gb|FL426696.1|FL426696
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|211126709|gb|FL428259.1|FL428259
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|211245303|gb|FL400469.1|FL400469
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|211070635|gb|FL369038.1|FL369038
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|32919174|gb|CF023986.1|CF023986
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|211455863|gb|FL399438.1|FL399438
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
EST: gi|71438969|gb|DR820019.1|DR820019
EST:     TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAG                         GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG
genomic: TGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG

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: 46 (upstream exon), 43 (downstream exon)
Score: 313

GGGACTTGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 677

GGGACTTGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 466

GGGACTTGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 648

GGGACTTGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttct ... tgtcctacagGTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACTTGACGCTCGTATCCCGCGGTCCGCCGCTGCGGGAGAGGGTCGACGGCAAGgtgaggttcttggaccgtctggccaaatttgtgtcctgcggtcgcgatcccagatcccatattgattccgttttttgctgttggtttcttggttgtcctacag

- - - - - - - - - - - - - - - - - - - GAGAGG