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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaacttccttgtgactccccaggggtcatgtttttttaagcaccgtctttcgacatcgattcagtaatactagtttccgtgtgcctcatttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAACAGCTGTATGCCCGTACGGGTAGACCCGAACTTCTGTAAAGATATTAAC

Basic information

species Zea mays
transcript GRMZM2G027821_T01
intron # 7
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|6022374|gb|AW067302.1|AW067302
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|211064881|gb|FL464879.1|FL464879
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTTACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|60357315|gb|DN224288.1|DN224288
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|88757593|gb|DY541734.1|DY541734
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTCACACCCCCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|211190398|gb|FL318556.1|FL318556
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGTGGAGCTTATA                         GCGAAAAGACGAAGGTTACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|211064880|gb|FL464878.1|FL464878
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTTACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|74235248|gb|DT643162.1|DT643162
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|32847753|gb|CD987434.1|CD987434
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTTACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|71434265|gb|DR815315.1|DR815315
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|78078285|gb|DV506700.1|DV506700
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTCACACCCCCACCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|211067604|gb|FL464880.1|FL464880
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTTACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
EST: gi|71328372|gb|DR800816.1|DR800816
EST:     CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA                         GCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA
genomic: CTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAA

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), 45 (downstream exon)
Score: 105

GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAACAGCTGTATGCCCGTACGGGTAGACCCGAACTTCTGTAAAGATATTAAC


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 55

GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAACAGCTGTATGCCCGTACGGGTAGACCCGAACTTCTGTAAAGATATTAAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 29

GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAACAGCTGTATGCCCGTACGGGTAGACCCGAACTTCTGTAAAGATATTAAC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 53

GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATAgtgagtttcc ... tttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAACAGCTGTATGCCCGTACGGGTAGACCCGAACTTCTGTAAAGATATTAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtctttcgacatcgattcagtaatactagtttccgtgtgcctcatttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAACAGCTGTATGCCCGTACGGGTAGACCCGAACTTCTGTAAAGATATTAAC
                                        cctcatttc  CT-rich tract
                     taatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaacttccttgtgactccccaggggtcatgtttttttaagcaccgtctttcgacatcgattcagtaatactagtttccgtgtgcctcatttcgtgcagGCGAAAAGACGAAGGTCACACCACCAGCATGCCAGTATATGGAGCACTGAACAGCTGTATGCCCGTACGGGTAGACCCGAACTTCTGTAAAGATATTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - ccttgtg
- - - - - - - - - - - - - - catgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgtgtgc