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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

Basic information

species Zea mays
transcript GRMZM2G378906_T01
intron # 3
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|32800512|gb|CD952748.1|CD952748
EST:     GTGGCTGTGAATACTGTGTTTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|32945507|gb|CF050326.1|CF050326
EST:     CTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: CTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|32933953|gb|CF038765.1|CF038765
EST:     GTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|32934625|gb|CF039437.1|CF039437
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|32799977|gb|CD952213.1|CD952213
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|13316152|gb|BG410599.1|BG410599
EST:     GTGGCTGTGAATACTGTGTATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTG-ATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|6194839|gb|AW146943.1|AW146943
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|6056701|gb|AW091106.1|AW091106
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|149101059|gb|EE187158.2|EE187158
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTTTGACACCCCC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|32788938|gb|CD941174.1|CD941174
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|32933749|gb|CF038561.1|CF038561
EST:     GTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|60336783|gb|DN203756.1|DN203756
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|211489683|gb|FL122966.1|FL122966
EST:     GATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|32913449|gb|CF018261.1|CF018261
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|148991091|gb|EE032539.2|EE032539
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|78022282|gb|DV490669.1|DV490669
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|211326076|gb|FL182495.1|FL182495
EST:     GKGGCTGKGAATACTGKGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
EST: gi|91054946|gb|EB165364.1|EB165364
EST:     GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTC                         TTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC
genomic: GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC

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: 39 (upstream exon), 47 (downstream exon)
Score: 407

GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 270

GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 371

GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 476

GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnn ... nnnnnnnnnnTTGAATCACATTATCAAGTCAACGAACATGAAATGTCTGACACCACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTGTGAATACTGTGATTCAGGATGAGAAGGAATTCnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

- - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - AAGGAA