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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaagccttgaaaaagtatgtcttatacttcatactactcagtcatgttgttattcgatggtgttatggtatttattggtttcgatctgaatggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG

Basic information

species Zea mays
transcript EF517601.1_FGT012
intron # 15
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 15
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 7
--------------------------------ttaagccttgaaaaagtatgtcttatacttc--atactactcagtcatgtt---gttattcgatggtgttatggtatttattggtttcgatctgaatggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG
                                  |   ||||  |  | |  |  ||||  |   || ||      | |||||   ||| |   ||| || | |  || | |||| | |  | |   |  ||| ||||||||||| ||||||||| | |||||||||||||||| |||||||||||| || ||||| ||||||||||| |||||
gtattcacagggttgagtggaagttggtgttgaaatatcttgttattgcaactactatatctgggatgctgtctgatgatgtttgtgttgtcacatgatgcttttctaatgattgatatgcacc---actgtg-cagGGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGG

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 15
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 7
ttaagccttgaaaaagtatgtcttatacttcatactactcagtcatgttgttattcgatggtgttatggtatttattgg---tttcgatctgaatggt-ggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG
       ||   |    |    |  |  |||  |    |   || | | ||| || ||| ||  |||| | ||| |  |   ||  | | | |  | |   ||||| ||||| ||||||||| ||||||| ||  | || ||||||||||| ||||| |||||||| |||||||| |||||
---gctattatcatttcaccattagtctttcccatagttgcatcgtttcgtt-ttggattgttatatgatttttttctgacattctgcttttatcgttcaacagGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG

upper sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 15
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 8
-----------ttaagccttgaaaaagtatgtcttatacttcatactactcagtcatgttgttattcgatggtgttatggtatttattggtttcgatctgaatggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG
           ||    ||||   || ||  | |   |||| | ||| ||  ||   | ||| ||||  |  | ||    ||||| ||  |||  ||        |||||||| ||||| |||||||| |||||||||||| | ||||| ||||||||||| || || || || |||||||| |||||
gcttgattttgtttcttcttgtgtaaatagatatacaactttacacttct-ggttg-gatgtcattctctaattttccattatttgttc-ttttaat--------tggcagGGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG

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:     TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|18385234|gb|BM418433.1|BM418433
EST:     ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|33093405|gb|CF053399.1|CF053399
EST:     TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|32944873|gb|CF049692.1|CF049692
EST:     ACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|33094530|gb|CF054524.1|CF054524
EST:     TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGTAGTANCT
genomic: TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|18384285|gb|BM417484.1|BM417484
EST:     ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|32932130|gb|CF036942.1|CF036942
EST:     ACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|19821794|gb|BQ047818.1|BQ047818
EST:     ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|22819752|gb|BU499842.1|BU499842
EST:     ACAAGG-GTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|17970295|gb|BM277058.1|BM277058
EST:     ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|33093018|gb|CF053012.1|CF053012
EST:     TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|87152447|gb|DY397236.1|DY397236
EST:     ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|19822007|gb|BQ048031.1|BQ048031
EST:     ACAAGGTGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|32943225|gb|CF048044.1|CF048044
EST:     TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|32910447|gb|CF015259.1|CF015259
EST:     ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|18384286|gb|BM417485.1|BM417485
EST:     ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: ACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|32930671|gb|CF035483.1|CF035483
EST:     TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: TACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
EST: gi|33094985|gb|CF054979.1|CF054979
EST:     GTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAG                         GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT
genomic: GTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCT

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: 603

TCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 335

TCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 258

TCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

TCTCATGAATATTGCTATGACTACTCTTAGTTCAAAAATACTTTCCCAAGACAAGGAGTACTTCGCTGAACTTGCGGTTGATGCTGTCTTGAGGCTTAAGgtatacaaat ... atggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttattcgatggtgttatggtatttattggtttcgatctgaatggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG
                  ttatggtatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaagccttgaaaaagtatgtcttatacttcatactactcagtcatgttgttattcgatggtgttatggtatttattggtttcgatctgaatggtggcagGGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - -gaaaaagt
- - - - - - - - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggtg