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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG

Basic information

species Zea mays
transcript GRMZM2G063909_T02
intron # 17
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|211314255|gb|FK994155.1|FK994155
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAANCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|60357508|gb|DN224481.1|DN224481
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|78076903|gb|DV505337.1|DV505337
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|60345083|gb|DN212056.1|DN212056
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|50331232|gb|CO526358.1|CO526358
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|40334210|gb|CK368280.1|CK368280
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACA                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|60400601|gb|DN233408.1|DN233408
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATATGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|60354991|gb|DN221964.1|DN221964
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|17932431|gb|BM269391.1|BM269391
EST:     GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: GACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
EST: gi|37394364|gb|CF634455.1|CF634455
EST:     CTTTGGACTATCTGAAACACG                         GTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA
genomic: CTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCA

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: 142

GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 241

GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 58

GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtttgt ... aactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG
                      cactcac  putative branch site (score: 77)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcagGTATCACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGGTAGGATCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC