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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccattttttctcggaacgtcttttgcagacatgttaagctgtttatgtgctgtatttatgaggccgttcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT

Basic information

species Zea mays
transcript GRMZM2G044348_T04
intron # 4
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|149012865|gb|EE042709.2|EE042709
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|211345313|gb|FL467149.1|FL467149
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|71435689|gb|DR816739.1|DR816739
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|148948442|gb|EC893960.2|EC893960
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|149027788|gb|EE286084.2|EE286084
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|148991460|gb|EE032969.2|EE032969
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCCAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|148948218|gb|EC893734.2|EC893734
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|32921110|gb|CF025922.1|CF025922
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|91875915|gb|EB405872.1|EB405872
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|149097124|gb|EE182936.2|EE182936
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|17930295|gb|BM267255.1|BM267255
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|149001048|gb|EE038297.2|EE038297
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|149100817|gb|EE186911.2|EE186911
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|78088713|gb|DV517106.1|DV517106
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|17930284|gb|BM267244.1|BM267244
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|149110465|gb|EE190430.2|EE190430
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGT
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGT
EST: gi|149067509|gb|EE157716.2|EE157716
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|148976595|gb|EE025942.2|EE025942
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|32921020|gb|CF025832.1|CF025832
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|31360319|gb|CD444676.1|CD444676
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|148943973|gb|EC889054.2|EC889054
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|211267467|gb|FK986909.1|FK986909
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTTCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|148930101|gb|EC872413.2|EC872413
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA
EST: gi|94475590|gb|EB704548.1|EB704548
EST:     AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTC                         CGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCCAAAGAGTGGAATGA
genomic: AACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGA

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: 49 (upstream exon), 49 (downstream exon)
Score: 115

TGCTTTTATCACTGTTCCTTCTATTCAAGTTTCTCTCAAAAGATTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

TGCTTTTATCACTGTTCCTTCTATTCAAGTTTCTCTCAAAAGATTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 193

TGCTTTTATCACTGTTCCTTCTATTCAAGTTTCTCTCAAAAGATTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

TGCTTTTATCACTGTTCCTTCTATTCAAGTTTCTCTCAAAAGATTTGGTCAACGCTGTGCTCACTGCCTACTTTTTCATTCTAGGCATTGTTGCTCTCTCgtaagtccat ... tcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcagacatgttaagctgtttatgtgctgtatttatgaggccgttcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT
                                         ccgttctt  CT-rich tract
 tgtatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccattttttctcggaacgtcttttgcagacatgttaagctgtttatgtgctgtatttatgaggccgttcttatgcagCGCAACACTGCTTCCTTCTATAAAACGTTTTCTTCCAAAAGAGTGGAATGATAATCTCATCGTCTGGCGGGCTCCATTCTTCCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA