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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagcagacaggttacattagtaaacactgttggtacagtgtacaccaactgtctttgactttctgcag

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgc--aagcagacaggtta----------cattagtaaacactgttggtacagtgtacacca-actgtctttgactttctgcag
|||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| || ||||||||||||   ||||    ||||           ||||||| |    | | |  || || |   ||| ||    |   || ||  ||||
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 21
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagcagacaggttacattagtaaacactgttggtacagtgtacaccaactgtctttgactttctgcag
||||||||||| || ||||| ||||| || ||||||||||| || || ||||||||  | || |||||||||||| | ||||||||| ||      ||       |||         | ||| | || || | |  |||| |  | |  ||  | |||
TGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttttaaccaagggtattgt---gttgtattgattcattgaatat-aactttactagctttgtttcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 22
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatg-----caagcagacaggttacattagtaaacactgttggtacagtgtacaccaa---ctgtctttgactttctgcag------------------
|||||||||||||| ||||||||||| || ||||| || || ||||| || ||||| || || |||||||| ||| | || |||||        || |      | ||| |||  |    | |  |  |    | ||    ||    | | ||| |   | |  ||                  
TGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgttgctttatcatgtcatttgtttatattcctttgaagttctcttttcctttattttaaatattatttttaatactttttagaattcatatgagccattt

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 19
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagcagacaggttacattagtaaacactgttggtacagtgtacaccaactgtctttgactttctgcag
|||||||| || || ||||| ||||| || ||||||||||| || || ||||||||  | || |||||||||||| | ||||||||| ||      ||   | |   || |      | ||| | || || |    |||| |  | |  ||  | |||
TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttttaac--ttaagggtattgttttgtattgattcattggatgt-aactttactagctttgtttcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 5'ss of exon 22
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagcagacaggttacattagtaaacactgttggtacagtgtacaccaactgtcttt--gactttctgcag---------------------
||||||||||| || |||||||| || || |||||||||||  |||||||||| ||||| || || || || ||| | |||||||||||     |||| | | | |  ||    || |    ||  | |  |   |   | |||||  || | |||   |                     
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAGgtatgttgctagac-gttaagaacagctctca-tacctgtttattacagttcctttttctttctgaatatcttttgaacgggatcaaaattatgtag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 23
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagcagacaggttacattagtaa-acactgttggtacagtgtacaccaactgt---ctttgactttctgcag
|||||||| || || ||||||||||| ||||| ||||||||||| || |||||||| || || |||||| ||||| | ||||| ||  ||   || | |  |    ||  | | | | |||| |     | |   |   || |   |||||  |      ||
TGGTTTGGAGAGGGCGAGAAGTATGTGAAGGCCGTTTTCTCACTTGCCAGTAAAATTGCTCCTAGTGTTGTATTTGTGGATGAAgtgagctt-catataactctttttgtttatatattgtttgcttcctctctgcttgctatattctttgtttggtcttag

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|22490580|gb|BU050503.1|BU050503
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|67025653|gb|CO454402.1|CO454402
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|87153787|gb|DY398576.1|DY398576
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|22490811|gb|BU050734.1|BU050734
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|211048834|gb|FL187594.1|FL187594
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATTGAAGCGAT
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCA-TGAAGCGAT
EST: gi|87152067|gb|DY396856.1|DY396856
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|19058833|gb|BM737500.1|BM737500
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|19058784|gb|BM737451.1|BM737451
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATG
EST: gi|211048836|gb|FL187596.1|FL187596
EST:     TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG                         GTCGATAGTATGC
genomic: TTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGC

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), 47 (downstream exon)
Score: 138

TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 185

TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 139

TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagc ... ctttctgcagGTCGATAGTATGCTAGGAAGGAGAGAAAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAGAATGAATTTATGGTAAATTGGGATGGACTGCGCACTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgcaagcagacaggttacattagtaaacactgttggtacagtgtacaccaactgtctttgactttctgcag

- - - - - - - - - - - - - - - - - - - - - - AGCAAG