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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATATCGATACGTTACTAGCTGCTGATGATAACTTTCTGCTGGGCCCCTGGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctacacatgcattcttcttcccccaacatctggatcctagatataccaatccccctttttctgctattgaggactggactgaactttttcaccag

Basic information

species Zea mays
transcript GRMZM2G033592_T01
intron # 17
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|211088560|gb|FL435458.1|FL435458
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACTGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|18168609|gb|BM338449.1|BM338449
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAGCGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGG--TGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|22549263|gb|BU101464.1|BU101464
EST:     AAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: AAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|20803078|gb|BQ294128.1|BQ294128
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|16926650|gb|BM079718.1|BM079718
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|211226693|gb|FL103755.1|FL103755
EST:     GTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|26559626|gb|CA831861.1|CA831861
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|26456384|gb|CA827967.1|CA827967
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|22818916|gb|BU499006.1|BU499006
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|78544545|gb|DV622043.1|DV622043
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|87157223|gb|DY402012.1|DY402012
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|5597242|gb|AI891235.1|AI891235
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGAGGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|5871470|gb|AW017941.1|AW017941
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|78021173|gb|DV489560.1|DV489560
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
EST: gi|32864143|gb|CF003825.1|CF003825
EST:     GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAG                         TACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG
genomic: GGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAG

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: 103

GGATATCGATACGTTACTAGCTGCTGATGATAACTTTCTGCTGGGCCCCTGGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GGATATCGATACGTTACTAGCTGCTGATGATAACTTTCTGCTGGGCCCCTGGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 190

GGATATCGATACGTTACTAGCTGCTGATGATAACTTTCTGCTGGGCCCCTGGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

GGATATCGATACGTTACTAGCTGCTGATGATAACTTTCTGCTGGGCCCCTGGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctaca ... ttttcaccagTACGAGTGGAACGCCAGAACACAGGTGACGATGTGGTATGACAACACGGAGACCGAGCAGAGTAAACTGCATGACTACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATATCGATACGTTACTAGCTGCTGATGATAACTTTCTGCTGGGCCCCTGGCTGGAAAGTGCAAAAAGCCTTGCTATAACTGAAAAGGAACGCCAGCAGgtatgctacacatgcattcttcttcccccaacatctggatcctagatataccaatccccctttttctgctattgaggactggactgaactttttcaccag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA