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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttgtgcttgcatcttgatctttgcagttttgtctacgtagcgagcgcccatttctcaatgatgctgttaaatctgttgcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGGCTCACCTGTGGACAGCAGATCAAGAAGTGGGAGCCCTTATGAGGATGGA

Basic information

species Zea mays
transcript GRMZM5G867185_T01
intron # 3
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|18173336|gb|BM348724.1|BM348724
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGATACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|211235330|gb|FL460963.1|FL460963
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|101389170|gb|EB816540.1|EB816540
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|17930469|gb|BM267429.1|BM267429
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|16920320|gb|BM074596.1|BM074596
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|211081539|gb|FL474813.1|FL474813
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTT-GAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|16919237|gb|BM074099.1|BM074099
EST:     GGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: GGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|19436505|gb|BM952915.1|BM952915
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|211433279|gb|FL466362.1|FL466362
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|71762469|gb|DR960406.1|DR960406
EST:     CCTCGTTATTATAGGGGCCGCTTTCCTTCACGCAGCCAAAGCTACTCGAG                         GTTTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTTCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|194717079|gb|FK934232.1|FK934232
EST:     CCTCGCTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|60343306|gb|DN210279.1|DN210279
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|93015739|gb|EB641259.1|EB641259
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|211231213|gb|FL350454.1|FL350454
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTTAGAGAGAGGTCCTACTCCG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTT-AGAGAGAGGTCCTACTCCG
EST: gi|78075881|gb|DV504315.1|DV504315
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|60342956|gb|DN209929.1|DN209929
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|211081538|gb|FL474812.1|FL474812
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTT-GAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|28982927|gb|BQ538413.2|BQ538413
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|211430917|gb|FL475029.1|FL475029
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|16919829|gb|BM074375.1|BM074375
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|32845885|gb|CD985566.1|CD985566
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|18165405|gb|BM335244.1|BM335244
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|50332884|gb|CO528010.1|CO528010
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|211240237|gb|FL479011.1|FL479011
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
EST: gi|17931670|gb|BM268630.1|BM268630
EST:     CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAG                         GTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG
genomic: CCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGG

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: 330

GGGTCATTCTTATGATGACAGGAGGTATTCTCGCTCTAGGTCGCCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGGCTCACCTGTGGACAGCAGATCAAGAAGTGGGAGCCCTTATGAGGATGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 119

GGGTCATTCTTATGATGACAGGAGGTATTCTCGCTCTAGGTCGCCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGGCTCACCTGTGGACAGCAGATCAAGAAGTGGGAGCCCTTATGAGGATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

GGGTCATTCTTATGATGACAGGAGGTATTCTCGCTCTAGGTCGCCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGGCTCACCTGTGGACAGCAGATCAAGAAGTGGGAGCCCTTATGAGGATGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

GGGTCATTCTTATGATGACAGGAGGTATTCTCGCTCTAGGTCGCCTCGTTATTATAGGGGCCGCTCTCCTTCACGCAGCCAAAGCTACTCGAGgtatgcttgt ... gcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGGCTCACCTGTGGACAGCAGATCAAGAAGTGGGAGCCCTTATGAGGATGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacgtagcgagcgcccatttctcaatgatgctgttaaatctgttgcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGGCTCACCTGTGGACAGCAGATCAAGAAGTGGGAGCCCTTATGAGGATGGA
                                tgttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttgtgcttgcatcttgatctttgcagttttgtctacgtagcgagcgcccatttctcaatgatgctgttaaatctgttgcattggtagGTCTCCACCTCAGAATCCAAGACACAGACTTAGAGAGAGGTCCTACTCCGGCTCACCTGTGGACAGCAGATCAAGAAGTGGGAGCCCTTATGAGGATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA