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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtgagtaccttttattgagtgttcttgcaggcatctatgtaattgttcccaacagaaaatgacactgatatctttttttatttgcttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG

Basic information

species Zea mays
transcript EF517601.1_FGT012
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os03g42220.2 (Oryza sativa), 3'ss of exon 7
ctgtgagtaccttttattgagtgttcttgcaggcatc-tatgtaattgttcccaacagaaaatgacactgatatctttttt---tatttgcttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
|  |||| |  |   |  |||||| || | |  ||   ||   || ||    | |  ||   |||  ||| | ||  |||    | || | ||||  | |  || |||||||||||||||||||||||  |||| || || ||| | |||||||||||||||||||| ||||||||||| |||||||||||||| ||||| |||
cactgagcaaat---acggagtgtactaggaaacactatacccaactgacaaccat-gattctgattctgctgtccgtttaacgttttggtttctgttttgcagTTTCATTCTTGACAAGAAAATTGGTCTTGGACAACCAAAGAGAATTGAGAATGCCAAAATTTTAGTTGCAAACACAGCTATGGACACAGACAAAGTAAAG

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
--ctgtgagtacctt-ttattgagtgttcttgca--ggcatctatgtaattgttcccaacagaaaatgacactgatatctttttttatttgcttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
   | | |  | ||| ||||| | | |||  |||  |      || | |||  ||     | ||| | |    | | ||||| | | |||  || ||  ||  || ||||||||||||||||||||||| ||||| || |||||||| || |||||||| || ||  |||| ||||||||||| ||||||||||| ||||| |||
tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaaagtaa----gctttctttctgtttttaattttttgat-cagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 9
-ctgtgagta--ccttttattgagtgttcttgcag-gcatctatgta-attgttcccaacagaaaatgacactgatatctttttttatttgcttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
    | ||||  | | ||||| | | | |  |||  || | |   |  |||  ||     | ||| | |      | ||| |||| | ||  || |  |    || ||||||||||||||||||||||| ||||| || ||||| || || |||||||| || ||  |||| ||||||||||| ||||||||||| ||||| |||
tgcattagtaatcttgttatttattttccaagcattgcttatccttgcattactctgggtaaaaagtaagctc--tgtctgttttaaatttgttttggt---cagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAACGTATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 16
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 8
---ctgtgagtaccttttattgagtgttcttgcaggcatctatgtaattgttcccaacagaaaatgaca-ctgatatctttttttatttgcttct-tatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
    |||   ||    | ||    | || |||        | |||   |  | | | |    |||     || || ||   |    ||    ||| |   | |||||| ||||||||||||||||| || ||||||||||| |||||||| |||||||| || || || || || || ||||||||||| || |||||||| |||
ggaatgttgatagtcatcatgtcatcttgttgtg-----ttgtgtttcttcttctatcgagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 16
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
ctgtgagtaccttttattgagtgttcttgcaggcatctatgtaattgttcccaacagaaaatgacactgatatctttttttatttg------cttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
       | |  | |    | |||  |  |       |    ||      || |   ||| | |     || | |||| ||| |||        | || |  ||||||| |||||||||||||| || |||||||| || || || ||||| |||||||| || |||||||| ||||| ||||| |||||||| |||||||| |||
-----cattctatattccaactgtcttctcttttcaattgtcaaacacatccgatgcaaattca-gtaaattttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG

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|33093211|gb|CF053205.1|CF053205
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|18385234|gb|BM418433.1|BM418433
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTNTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|33093405|gb|CF053399.1|CF053399
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|32944873|gb|CF049692.1|CF049692
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|33094530|gb|CF054524.1|CF054524
EST:     ATTCTGAAGAAACCTGTAGTANCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGGCAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|18384285|gb|BM417484.1|BM417484
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|32932130|gb|CF036942.1|CF036942
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|19821794|gb|BQ047818.1|BQ047818
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|22819752|gb|BU499842.1|BU499842
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|17970295|gb|BM277058.1|BM277058
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|33093018|gb|CF053012.1|CF053012
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|87152447|gb|DY397236.1|DY397236
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|19822007|gb|BQ048031.1|BQ048031
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|32943225|gb|CF048044.1|CF048044
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|32910447|gb|CF015259.1|CF015259
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|18384286|gb|BM417485.1|BM417485
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|32930671|gb|CF035483.1|CF035483
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
EST: gi|33094985|gb|CF054979.1|CF054979
EST:     ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG                         GTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA
genomic: ATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAA

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: 47 (upstream exon), 49 (downstream exon)
Score: 351

GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 166

GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 143

GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgtattt ... ttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcccaacagaaaatgacactgatatctttttttatttgcttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG
                   cactgat  putative branch site (score: 143)
                         tatctttttttatttg  CT-rich tract
                        atatctttttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtgagtaccttttattgagtgttcttgcaggcatctatgtaattgttcccaacagaaaatgacactgatatctttttttatttgcttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG

- - - - - - - - - - - - - -tgcaggc
- - - - - - - - - - - - - - - - - - - - - - - - - -caacaga