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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGGTGCCACACCTGGGCACCCAGGCATGGGTCAGGTCCCTCAACTTCCCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatatatatacatacacacaatctccctgtcctgatcttcaggcctctttgattgttgccaattgaactttctatttctttttctgttcgttgaggatgatattgattccttcatgcgcgtgtcgctgttcttgcttcgcgcag

Basic information

species Zea mays
transcript GRMZM2G471269_T04
intron # 12
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|71762617|gb|DR960554.1|DR960554
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|5108189|gb|AI739902.1|AI739902
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|37392581|gb|CF633542.1|CF633542
EST:     TGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACCACATGACGTTCGCGACGATCAAA
genomic: TGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|78027468|gb|DV495855.1|DV495855
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|78111058|gb|DV529455.1|DV529455
EST:     CCCGTTGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|78120814|gb|DV539198.1|DV539198
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|148949256|gb|EC894699.2|EC894699
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|116827409|gb|EC871310.1|EC871310
EST:     GGCG-GGCATCTC-GTGGCC-AG-CGCCGG                         G-TCACGATAAATTACTCAAAC-ACATGACGTTCGCGACGATCAAA
genomic: GGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|110533510|gb|EE037690.1|EE037690
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|14203015|gb|BG836692.1|BG836692
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|78083939|gb|DV512332.1|DV512332
EST:     CCCGTCGTCGACGACTGGAGGGGGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|211272707|gb|FL458993.1|FL458993
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTTGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|211231289|gb|FL464293.1|FL464293
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|16919289|gb|BM074120.1|BM074120
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|88750452|gb|DY534593.1|DY534593
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|111145649|gb|EE257973.1|EE257973
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|5069690|gb|AI737655.1|AI737655
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|8401242|gb|BE056876.1|BE056876
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|86468083|gb|DY234453.1|DY234453
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|71299116|gb|DR785562.1|DR785562
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|211175969|gb|FL481229.1|FL481229
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|74233921|gb|DT641835.1|DT641835
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|110516814|gb|EE021401.1|EE021401
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|78026574|gb|DV494961.1|DV494961
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|78125073|gb|DV543457.1|DV543457
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCCCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|148966524|gb|EE017546.2|EE017546
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCNAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|37397736|gb|CF636176.1|CF636176
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACTATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA
EST: gi|40337181|gb|CK371251.1|CK371251
EST:     CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGG                         GTTCACGATAAATTACTCAAACAACATGACGTTCGCGACTATCAAA
genomic: CCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA

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: 47 (upstream exon), 47 (downstream exon)
Score: 20

TGCTGGTGCCACACCTGGGCACCCAGGCATGGGTCAGGTCCCTCAACTTCCCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

TGCTGGTGCCACACCTGGGCACCCAGGCATGGGTCAGGTCCCTCAACTTCCCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

TGCTGGTGCCACACCTGGGCACCCAGGCATGGGTCAGGTCCCTCAACTTCCCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 46

TGCTGGTGCCACACCTGGGCACCCAGGCATGGGTCAGGTCCCTCAACTTCCCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatat ... cttcgcgcagGTTCACGATAAATTACTCAAACAACATGACGTTCGCGACGATCAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGGTGCCACACCTGGGCACCCAGGCATGGGTCAGGTCCCTCAACTTCCCCGTCGTCGACGACTGGAGGGCGTGGCATCTCGGTGGCCAAGCCGCCGGgtgggtatatatatacatacacacaatctccctgtcctgatcttcaggcctctttgattgttgccaattgaactttctatttctttttctgttcgttgaggatgatattgattccttcatgcgcgtgtcgctgttcttgcttcgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG