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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtttcatgcaattgtctcatatcatatgcttaagagggcagggttatctgaacatcagtgctgtgagatctggtcgatgtcttgtgcttattaatccttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTT

Basic information

species Zea mays
transcript GRMZM2G179308_T01
intron # 10
splice site 3'
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|32807402|gb|CD959636.1|CD959636
EST:     ATGGAGGGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|32787565|gb|CD936467.1|CD936467
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACCCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|45568628|gb|CK986157.1|CK986157
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCGTACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|76015336|gb|DT942506.1|DT942506
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|71756384|gb|DR954321.1|DR954321
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|211191418|gb|FL472415.1|FL472415
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAATTACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|76015337|gb|DT942507.1|DT942507
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|211429794|gb|FL437778.1|FL437778
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|211241890|gb|FL451479.1|FL451479
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|60357877|gb|DN224850.1|DN224850
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|33096467|gb|CF056461.1|CF056461
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|60347445|gb|DN214418.1|DN214418
EST:     ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|166414524|gb|EG248328.1|EG248328
EST:     ACCTTTGCCGTACCATATGTTCAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGGGGG
genomic: ACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG

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), 48 (downstream exon)
Score: 373

GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 295

GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTT


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 388

GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTT


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 290

GGTGAGGCGATATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGGGTTCTTGGACCTTTGCCATACCATATGTTCAAGAGGGCAGAgtacgtttca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcagtgctgtgagatctggtcgatgtcttgtgcttattaatccttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTT
                                    tattaat  putative branch site (score: 290)
                                          tccttgttt  CT-rich tract
                                   ttattaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtttcatgcaattgtctcatatcatatgcttaagagggcagggttatctgaacatcagtgctgtgagatctggtcgatgtcttgtgcttattaatccttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGGTTGCACTTCGCGTGAAAGCATGAAAGCTGTGATGAAATTGTCCAGGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG