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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatttcagtccttgaaaaagagcacggcaccatattttttcccccctgttttgtaagtaagataagaagcaagtatggttttttctgcaattgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGACAGAAAACCGAAGGTTACAAGGAAGCACGGATGCATATAATGTCTGTCT

Basic information

species Zea mays
transcript GRMZM2G021864_T01
intron # 19
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|33091337|gb|CF051331.1|CF051331
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|211215778|gb|FL437224.1|FL437224
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|32909144|gb|CF013956.1|CF013956
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACCCGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|89248917|gb|DY620703.1|DY620703
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|5608024|gb|AI901691.1|AI901691
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|6194461|gb|AW146565.1|AW146565
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCACCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|32934210|gb|CF039022.1|CF039022
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTAC
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTAC
EST: gi|78106767|gb|DV525185.1|DV525185
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|116827696|gb|EC871624.1|EC871624
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|32930527|gb|CF035339.1|CF035339
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTAC
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTAC
EST: gi|32932800|gb|CF037612.1|CF037612
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTA
EST: gi|5713643|gb|AI943635.1|AI943635
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|113687140|gb|DW842602.1|DW842602
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACG
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACG
EST: gi|32932808|gb|CF037620.1|CF037620
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTA
EST: gi|91054831|gb|EB165249.1|EB165249
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
EST: gi|13381810|gb|BG458485.1|BG458485
EST:     GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAG                         GGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA
genomic: GCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGA

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), 46 (downstream exon)
Score: 117

ACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGACAGAAAACCGAAGGTTACAAGGAAGCACGGATGCATATAATGTCTGTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 72

ACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGACAGAAAACCGAAGGTTACAAGGAAGCACGGATGCATATAATGTCTGTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

ACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGACAGAAAACCGAAGGTTACAAGGAAGCACGGATGCATATAATGTCTGTCT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 80

ACCTGGAGCTTGAGCTGGAGGAAACAAAAAAGAAGTGCGGTCAGCTTGCTGCTCAGCTCAAGGCATGGAAGAACCAGCAGCATCTACCCTAAATGTGAAGgttagtttgg ... attgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGACAGAAAACCGAAGGTTACAAGGAAGCACGGATGCATATAATGTCTGTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttttgtaagtaagataagaagcaagtatggttttttctgcaattgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGACAGAAAACCGAAGGTTACAAGGAAGCACGGATGCATATAATGTCTGTCT
             taagataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatttcagtccttgaaaaagagcacggcaccatattttttcccccctgttttgtaagtaagataagaagcaagtatggttttttctgcaattgctgcagGGCATCATTAAGACCGAGGACACGGAGGTACACGACAACGACCAATACTGACAGAAAACCGAAGGTTACAAGGAAGCACGGATGCATATAATGTCTGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - gtccttg
- - - - - - - -aaaaaga
- - - - - - - - - - - - -cggcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgca