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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGAGGAGCCATAGTTGAAACAATCTATCTGCTGCAGCCCCACACCCCAGTTA

Basic information

species Zea mays
transcript GRMZM2G145595_T02
intron # 13
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|211470347|gb|FL451278.1|FL451278
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|20512800|gb|BQ279999.1|BQ279999
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|13249875|gb|BG360780.1|BG360780
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|211093993|gb|FL455618.1|FL455618
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|37377273|gb|CF625226.1|CF625226
EST:     CACACCCAACGTTGTGTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|211470346|gb|FL451277.1|FL451277
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|16378429|gb|BI992442.1|BI992442
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|6865111|gb|AW360461.1|AW360461
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|13249874|gb|BG360779.1|BG360779
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|6672118|gb|AW282293.1|AW282293
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|32830615|gb|CD970293.1|CD970293
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|26456706|gb|CA828289.1|CA828289
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|20512799|gb|BQ279998.1|BQ279998
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|6563894|gb|AW231516.1|AW231516
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|32830552|gb|CD970230.1|CD970230
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|211093994|gb|FL455619.1|FL455619
EST:     GTTGTTTGAAGATCTGGATGAACTTTTCAAGGCTGCCAAA                         GTTAACACAGCCGGTTTGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: GTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|32831600|gb|CD971278.1|CD971278
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
EST: gi|211093992|gb|FL455617.1|FL455617
EST:     CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG                         GTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA
genomic: CACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGA

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), 48 (downstream exon)
Score: 26

GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGAGGAGCCATAGTTGAAACAATCTATCTGCTGCAGCCCCACACCCCAGTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 26

GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGAGGAGCCATAGTTGAAACAATCTATCTGCTGCAGCCCCACACCCCAGTTA


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 10

GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGAGGAGCCATAGTTGAAACAATCTATCTGCTGCAGCCCCACACCCCAGTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 21

GACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAGgtacatgtgc ... ccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGAGGAGCCATAGTTGAAACAATCTATCTGCTGCAGCCCCACACCCCAGTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGAGGAGCCATAGTTGAAACAATCTATCTGCTGCAGCCCCACACCCCAGTTA
                              ccttgac  putative branch site (score: 21)
                           ttgccttgaccttttt  CT-rich tract
                   aacaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatgtgcctatttgcccttatgctatatagtatatacataaatgattctttgtgtgaaaaatacaaacaaaatttgtgccctgtaccaaaaacgtgaacaaaaattgccttgacctttttctccttcaacagGTTAACACAGCTGGTTCGCATTCTATGAATGAGCCAGTTGCGGTGTAGAGAGGAGCCATAGTTGAAACAATCTATCTGCTGCAGCCCCACACCCCAGTTA

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