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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccatcttccccccttcatcttttgtggtaaccctatggtttctcttatgccattgttattgtcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGCTAC

Basic information

species Zea mays
transcript GRMZM2G035417_T01
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|60356802|gb|DN223775.1|DN223775
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|211524990|gb|FL195258.1|FL195258
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGCCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|5932681|gb|AW057042.1|AW057042
EST:     GTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|71448259|gb|DR829309.1|DR829309
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|78121958|gb|DV540342.1|DV540342
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|120480604|gb|EH210908.1|EH210908
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|211521980|gb|FL195242.1|FL195242
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGCCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|78107573|gb|DV525991.1|DV525991
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|9825075|gb|BE575292.1|BE575292
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACG
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACG
EST: gi|5566780|gb|AI881646.1|AI881646
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|94472331|gb|EB701289.1|EB701289
EST:     CATCAGTTGCAAGAAACACCA-CACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCCTCCA-GTGTCCAACCTCANGCTGCTCCAGCTGCTACGGTTGCTG
genomic: CATCAGTTGCAAGAA-CACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACC-TCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTG
EST: gi|20803264|gb|BQ294314.1|BQ294314
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|91876714|gb|EB406671.1|EB406671
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|74244160|gb|DT652074.1|DT652074
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
EST: gi|76908411|gb|DV162927.1|DV162927
EST:     GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAAC                         GGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC
genomic: GCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGC

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: 48 (upstream exon), 49 (downstream exon)
Score: 305

GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 470

GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGCTAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 392

GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGCTAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 377

GCCCAACCTGCTGCCCCTGTGGCCCCTGCTGCATCAGTTGCAAGAACACCAACACAGGCTCCTGTTGCCACAGCTGAAACgtgagccatc ... tcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGCTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttgtggtaaccctatggtttctcttatgccattgttattgtcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGCTAC
                                          ttgtctt  CT-rich tract
                                   attgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccatcttccccccttcatcttttgtggtaaccctatggtttctcttatgccattgttattgtcttacacagGGCACCTCCAAGTGTCCAACCTCAGGCTGCTCCAGCTGCTACGGTTGCTGCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT