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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgcatttactcatttgccaaaattgcgcacctctttctcttcgatatatatccactccgctgatccacaaacatgcaaaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAGTATATCGACCTGAGAAAGGATTAAGCCAACACTTCAGTTGTGCTGCAGC

Basic information

species Zea mays
transcript GRMZM5G817037_T02
intron # 6
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|78118564|gb|DV536948.1|DV536948
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|211427863|gb|FL460787.1|FL460787
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|71433500|gb|DR814550.1|DR814550
EST:     ATTTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|71433501|gb|DR814551.1|DR814551
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|149105264|gb|EE290754.2|EE290754
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|32848620|gb|CD988301.1|CD988301
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGT
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGT
EST: gi|50339217|gb|CO534343.1|CO534343
EST:     ATCTAATTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCG
EST: gi|148953910|gb|EC899291.2|EC899291
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|60397822|gb|DN230638.1|DN230638
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|211427862|gb|FL460786.1|FL460786
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|31250194|gb|CD219218.1|CD219218
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|7009428|gb|AW455693.1|AW455693
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGCTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|33100971|gb|CF060931.1|CF060931
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|18174710|gb|BM350098.1|BM350098
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|32858194|gb|CD997875.1|CD997875
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAAC
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAAC
EST: gi|148965092|gb|EE015909.2|EE015909
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|31352578|gb|CD436935.1|CD436935
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTAAGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|5456196|gb|AI833886.1|AI833886
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|149105265|gb|EE290755.2|EE290755
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGGCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|32859552|gb|CD999233.1|CD999233
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|148930814|gb|EC873185.2|EC873185
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|91868767|gb|EB400150.1|EB400150
EST:     ATCTAGTCAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|37398186|gb|CF636403.1|CF636403
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|32858122|gb|CD997803.1|CD997803
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|71433723|gb|DR814773.1|DR814773
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|148965093|gb|EE015910.2|EE015910
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCG
EST: gi|6695570|gb|AW288678.1|AW288678
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|31351401|gb|CD435758.1|CD435758
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTAAGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG
EST: gi|31356308|gb|CD440665.1|CD440665
EST:     ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACT                         GGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTAAGCGCGAG
genomic: ATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAG

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: 227

GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAGTATATCGACCTGAGAAAGGATTAAGCCAACACTTCAGTTGTGCTGCAGC


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

GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAGTATATCGACCTGAGAAAGGATTAAGCCAACACTTCAGTTGTGCTGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 63

GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAGTATATCGACCTGAGAAAGGATTAAGCCAACACTTCAGTTGTGCTGCAGC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 113

GATGCTGTCACACCATTGTCGGAGTCAGAGGCCATCGATCTAGTTAAGGACGTGTTCGCATCTGCAACTGAGAGAGACATCTACACTgtaagctgca ... aaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAGTATATCGACCTGAGAAAGGATTAAGCCAACACTTCAGTTGTGCTGCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctcttcgatatatatccactccgctgatccacaaacatgcaaaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAGTATATCGACCTGAGAAAGGATTAAGCCAACACTTCAGTTGTGCTGCAGC
                         cgctgat  putative branch site (score: 113)
           atatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgcatttactcatttgccaaaattgcgcacctctttctcttcgatatatatccactccgctgatccacaaacatgcaaaatatgcagGGAGACAAGTTGGAAATTGTAGTCATTAACAAGGCCGGTACTATGCGCGAGTATATCGACCTGAGAAAGGATTAAGCCAACACTTCAGTTGTGCTGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG