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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagtttttcccattaacaaatctgtgagcacacaaggttactggggcccctttgtgtt...

Basic information

species Zea mays
transcript GRMZM2G019267_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 5'ss of exon 8
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgta--gattttttcagtctt---tcgtgtgttagtttacggttttttcagtttttcccattaacaaatctgtgagcacacaaggttactggggcccctttgtgtt
 || ||||| | |||||| |||||||||||||||||||||||||| ||||||||||| || ||||||||||| |||||||||||| | |||||||||||||||  |  | ||  ||  ||      |   || | | || |   |  |  |   |   | |     || |     |  |     ||| | | ||   |       
CGGGAGCACGAGGTATGGTCCAGCCGTTGACATGTGGTCAGTGGGTTGTATTTTTGCTGAGCTTCTCAATGGAAAGCCAATATTGACAGGAAAGAATGAGgtattgcatcttgaagctttgagctatcaattggataactgaagtgccgttgcattttagtttttcatttccctccttagtgcattatttgtgctgatac-----

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G04410.1 (Glycine max), 5'ss of exon 8
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagtttttcccattaacaaatc-tgtga-gcacacaaggttactggggcccctttgtgtt--
 ||||  ||||||||||| ||||| || || |||||||| || || || |||||||| || |||||  | |||||||| ||||| ||||||||  |||||||   |  |     | |   || || ||| | |  |   ||  || |      || ||  | |  |||||     |  | |     |       |||   ||  
AGGAACAACAAAGTATGGGCCAGCTGTGGATATGTGGTCTGTTGGGTGCATTTTTGCTGAGCTTCTTCAAGGGAAGCCTATATTTCCTGGAAAAGATGAGgttagtgat----atttaatgtatgataggtcagagaaattagagctggattgatgaatgattggtgtgatattgattatgggctagatatggttttaactttt

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G10960.1 (Glycine max), 5'ss of exon 7
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgta---gattttttcagtctttcgtgtgttagtttacggttttttcagtttttcccattaacaaatctgtgagcacacaaggttactggggcccctttgtgtt-
||| |  |||| |||||| ||||| || || |||||||| || || || ||||||||||| |||||  |||||||||| || || ||||||||  |||||||    |||  | |   |  ||| ||| | |  ||| || |     |    |     | ||    | |    ||     | | |  |      ||  | |||| 
TGGGACAACAAGGTATGGGCCAGCTGTAGATATGTGGTCTGTAGGGTGCATTTTTGCAGAGCTTCTTCATGGGAAGCCTATCTTTCCTGGAAAAGATGAGgttagtgataatatgtataattcttgtctgaaattaggggtaaagtaaaagtggttgtgaaattgtattgtggcgaggcatgctttta----tccagtatgtta

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT5G64960.2 (Arabidopsis thaliana), 5'ss of exon 7
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagtttttcccattaacaaatctg-tgagcacacaaggttactggggcccctttgtgtt
|||    || || ||||| |||||  |||||||||||||||| || || || ||||| |||||| | ||||| || ||||| |||||||| || | ||||||     |||    |  |   | |  | || |  | || || |||| ||      | |    ||   | |||     || | |         ||||     
TGGTGCAACTAAATATGGACCAGCGATTGACATGTGGTCAGTTGGATGCATATTTGCTGAACTTTTGAATGGAAAACCAATCTTGCCTGGGAAAACTGAGgtcaggatttcatcttatgattatcgtggtgtgtg-ttattacagtgttctttgatgatgtttccacttagcgttttag-tcatatttttttctttccag-

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 5'ss of exon 9
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagttt------ttcccattaacaaatctgtgagcacacaaggttactggggcccctttgtgtt
||| | ||||| |||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||  |||| || || || || ||||||||  ||||||||| ||  | |     ||  |||  |   ||  ||||     ||||       |||   | | ||| | |    | ||| |   ||  |  || |   | ||   
TGGGACCACAAGGTATGGTCCAGCTGTTGATATGTGGTCAGTTGGCTGTATCTTTGCAGAACTTCTGCATGGAAAACCTATCTTTCCTGGAAAAGATGAGgtaggttgctcc--ctattgatgtcatttcttttggttggaatagttggtgagattcttttaatcaagtgtacttgaacaaataatt--taaggactgatggtc--

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 5'ss of exon 7
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagtttttcccattaacaaatctgtgagcacacaaggttactggggcccctttgtgtt-
 ||   ||||||||||   ||||| || ||||||||||||||||| || |||||||| || ||||| |||||||| || ||  | || |||| ||| |||||     |||  | ||       ||     ||    |||     | |  |||   |  ||   ||||           ||     |      |   |  | 
GGGCTCCACAAAGTATACTCCAGCTGTGGACATGTGGTCAGTGGGGTGCATTTTTGCTGAGCTTCTTAATGGGAAACCCATCCTTCCCGGAAGGAACGAGgtgtgactttagattcacagaactgcggccttctcatttggattgatgatcctgctt-cagtcctgtttagggttggagtggtcagatgttttcgatagta

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: PP1S235_102V6.1 (Physcomitrella patens), 5'ss of exon 7
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagttttt--cccattaacaaatctgtgagcacacaaggtta--ctggggcccctttgtgtt
 ||   ||| |||||    |||||||| ||||||||||||||||| ||||||||||| || |||||||| ||||| || ||  | || |||| ||| |||||    ||    ||||||     |||   | | | |||         ||       |||||     | | |  || |    |||   | ||      || |   
GGGTTCCACCAAGTACACTCCAGCCGTGGACATGTGGTCAGTGGGATGTATTTTTGCCGAGCTTCTCAACGGGAAACCCATTCTTCCCGGAAGGAACGAGgtgtgattaaggagtcttctcgttgtctttcttcagttacgcagaacttcaatgtgttaacgtggat-taatgactctgccttagatttggatgaacttat---

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: EFJ34303 (Selaginella moellendorffii), 5'ss of exon 6
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagtttttcccattaacaaatctgtgagcacacaaggttactggggcccctttgtgtt
|||  | ||||||||||| ||||| || ||||||||||| |||||||| || |||||||| |||||| | || |||||| | ||  | ||||| ||||||||          ||||| |||| | | ||||| | |  | ||   ||| || |  |  ||                                        
TGGCTGTACAAAGTATGGGCCAGCAGTAGACATGTGGTCTGTGGGCTGCATCTTTGCAGAGCTTCTCTACGGAAAGCCAGTGTTAACGGGAAAAAATGAGgtgagcggcg--agtctctcgtatatgagttttctgactcttt--tttctctcgcttccag---------------------------------------

upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 7
lower sequence: EFJ31297 (Selaginella moellendorffii), 5'ss of exon 7
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagtttttcccattaacaaatctgtgagcacacaaggttactggggcccctttgtgtt
|||  | ||||||||||| ||||| || ||||||||||| |||||||| || |||||||| |||||| | || |||||| | ||  | ||||| ||||||||          ||||| |||| | | | ||| | |  | ||    ||||| |  |  ||                                        
TGGCTGTACAAAGTATGGGCCAGCAGTAGACATGTGGTCTGTGGGCTGCATCTTTGCAGAGCTTCTCTACGGAAAGCCAGTGTTAACGGGAAAAAATGAGgtgagcggcg--agtctctcgtatatgacttttctgactctt----ttttctcgcttccag---------------------------------------

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|71766382|gb|DR964319.1|DR964319
EST:     TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA
EST: gi|93282558|gb|EB674822.1|EB674822
EST:     TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA
EST: gi|149107723|gb|EE189597.2|EE189597
EST:     TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCCAGCTTTGTGGTACCCC
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCC
EST: gi|149099519|gb|EE185557.2|EE185557
EST:     TTTTTGCAGAACTTCTCAATGGGGAGCCAATATTGCCTGNAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATG
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATG
EST: gi|32844191|gb|CD983872.1|CD983872
EST:     TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTA
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTA
EST: gi|148969561|gb|EE020392.2|EE020392
EST:     TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA
EST: gi|211325352|gb|FL255515.1|FL255515
EST:     TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA
EST: gi|32845306|gb|CD984987.1|CD984987
EST:     TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTA
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTA
EST: gi|149106097|gb|EE291761.2|EE291761
EST:     TTTTTGCAGAACTTCTCAATGGGGAGCCAATATTGCCTGGAAAGAATGAG                         CCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACC
genomic: TTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACA

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: 393

TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACAATCTGGCCTGGTGTCACAAAAATGCCTTGGTACAACAACTTCAAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACAATCTGGCCTGGTGTCACAAAAATGCCTTGGTACAACAACTTCAAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 363

TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACAATCTGGCCTGGTGTCACAAAAATGCCTTGGTACAACAACTTCAAGCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttt ... attcctgcagCCAGAGCAGCTGACTAAGATCTTCGAGCTTTGTGGTACCCCTGATGACACAATCTGGCCTGGTGTCACAAAAATGCCTTGGTACAACAACTTCAAGCCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAAGCACAAAGTATGGCCCAGCCGTTGACATGTGGTCAGTGGGCTGTATTTTTGCAGAACTTCTCAATGGGAAGCCAATATTGCCTGGAAAGAATGAGgtagattttttcagtctttcgtgtgttagtttacggttttttcagtttttcccattaacaaatctgtgagcacacaaggttactggggcccctttgtgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA