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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcgcttacttaagaatccacattgtatatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt...

Basic information

species Zea mays
transcript GRMZM2G303631_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g20630.1 (Oryza sativa), 5'ss of exon 2
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcg--cttacttaagaatccacattgtatatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt
||| |||||||||||||||| |||||||||||||||||||| ||||||||||| || ||||| || || |||||||||||||||||||||||||||||||||| | ||   |||  || ||    ||| | |  | ||  |   |    ||   | | ||||  || |||  |||  |   |   | | |||  |    |  
TGGATCTGGTGGGATTATGTAACTGATTTTCACATAAGGTGCCCAATGAAGGACAAAAAGTATAACAAGAAATGTGCAGAAACTGTCATCAAATCACTAGgttggttcttcttttgtttctgagactttcctttgcata-atgataagcatgattgtagtaattacttgtacgtacttaaattggacgtttgaaatatgcc-

upper sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G00370.1 (Glycine max), 5'ss of exon 2
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcgcttacttaagaatccacattgt-atatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt
||||| |||||||||||||| ||||||||||| || || || || |||||||| || |||||||||||  |||||||| |  |||| || |||||||| |||    |   |   | |  |    |   || |   | ||    || |||   | |||   |   | | | |  ||  |||  |                  
TGGGTGTGGTGGGATTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGACAACAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgtaaattaaatcaccatcgcatcttatttttatcttacagggggtgataatgactttactattgcgtttcttcaatatttgcag-----------------

upper sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G40340.1 (Glycine max), 5'ss of exon 2
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtt--tgctccgttttctttcctcgcttacttaagaatccacattgtatatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt----
||||| |||||||| ||||| ||||||||||| || || || |||||||||||||| ||||| || || |||||||| ||  |||||||  ||||||| ||    ||   |  ||  || | |  | |  ||     |     |||   ||   || |  |  |  ||  ||     | |  || ||| ||       |  |    
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCAATGAAGGAGAAAAAGTATAACAAGAAATGTGCTGATGCTGTCATTGAATCACTTGgcaagtgaatctattatttgcttatcatgttttcctttagtggttgaggatgacttctcaattatgattattcagtatctcaaatatgattattcaatatctgcag

upper sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G27000.1 (Glycine max), 5'ss of exon 2
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgtt-ttctttcctcgcttacttaagaatccacattgtatatatattttgtaaaaacatgtttgtaa-gtttttaacatgcttggcacccactt----
||||| |||||||| ||||| ||||||||||| || || || |||||||||||||| || || || || |||||||| ||  |||||||  ||||||| ||   |      | || ||| ||   |   ||     |    | |  ||    | ||   ||| |    | |  |   | |  || ||| ||       |  |    
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCAATGAAGGAGAAAAAATATAACAAGAAATGTGCTGATGCTGTCATTGAATCACTTGgcaagtgaatctgttatttgcttattatgttttctgttagtagttgatgatgacttctcaaatatgattattcagtatctcaaatatgattattcaatatctgcag

upper sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G45380.1 (Glycine max), 5'ss of exon 2
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcgcttacttaagaatcca-cattgtatatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt
||||| |||||||| ||||| ||||||||||| || || || || |||||||||||||||||||||||  |||||||| |  |||| || |||||||| |||    |   |   | |  | ||||   || |   | || ||| |   ||      | ||  |  | ||||||  | | |   ||                
TGGGTGTGGTGGGACTATGTCACTGATTTTCAAATTAGATGCCCCATGAAGGAGAAGAAGTACAATAAGGAATGTGCAAATGCTGTTATTAAATCACTGGgta-aataaatcaccatcgcacgctatttttatcttacagcatggctgatgatgactttactattacgtttgttcgatatctgcag---------------

upper sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G14720.1 (Arabidopsis thaliana), 5'ss of exon 2
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcgcttacttaagaatccacattgtatatatattttgtaaaaacatgtttgtaagtttttaacatg-cttggcacccactt
|||||||||||||||||||| |||||||| || || || ||||||||||||||||| || ||||| ||| | ||||| ||  |||| |||||||| || |||  |    ||||  | |    | |  ||  | | |  | |    |   |  |||||  | ||   | |  ||  || |    ||| |    ||       
TGGGTCTGGTGGGATTATGTTACTGATTTCCAGATCAGATGTCCAATGAAGGAGAAAAAATACAACAAAGATTGTGCTGAGTCTGTAATCAAATCTCTTGgtgagt---gtttcttcttacaggt--ctcgatagttga-aagaaaagcaatttttgggagaatgaggtcatattttctatgtatgtccctacag------

upper sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT2G14740.2 (Arabidopsis thaliana), 5'ss of exon 2
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcgcttacttaagaatccacattgtatatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt
|||||||||||||||||||| |||||||| || || || ||||| |||||||||||||| ||||||||  | ||||| ||  | || |||||||| || |||  |    || |   ||    ||  | | |||||     ||| |    | | |      |  |||  ||   |  | || |||                
TGGGTCTGGTGGGATTATGTTACTGATTTCCAGATCAGATGTCCCATGAAGGAGAAGAAATACAATAAGGAGTGTGCTGATTCCGTTATCAAATCTCTTGgtgagt---gtgtctgttatatgcaaattaaagaaagacaattttggggagaat-----gatgcatagttactatgtctttacag---------------

upper sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 5'ss of exon 2
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcgcttacttaagaatccacattgtatatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt
||||| |||||||| ||||||||||||||||| || || ||||| |||| | |||| || ||||| ||  ||||||| ||||||||||||  ||| ||||||        | | ||| | ||   |  ||   |    ||     |||| |  ||  |||     | ||| ||| | ||     |||   |         
TGGGTGTGGTGGGACTATGTGACTGATTTTCAAATTAGATGTCCCATGAGGAAGAAAAAATACAACAAGGAATGTGCTGAAACTGTCATCGCATCTCTAGgtaaataatatatccttgcatcctctgattgtaaggataccagtcatat-tgattaataattttttatttctaa-tgttggttctgcacag---------

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|5847202|gb|AW000281.1|AW000281
EST:     GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
EST: gi|5325106|gb|AI783297.1|AI783297
EST:     GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
EST: gi|211449604|gb|FL033165.1|FL033165
EST:     AGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTTGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: AGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
EST: gi|5325027|gb|AI783218.1|AI783218
EST:     GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
EST: gi|211156293|gb|FL375842.1|FL375842
EST:     ATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTTGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: ATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
EST: gi|32850609|gb|CD990290.1|CD990290
EST:     AAAATGTGCAGAAACTGTCATCAAATCATTAG                         GTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: AAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
EST: gi|91054221|gb|EB164639.1|EB164639
EST:     GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
EST: gi|5846840|gb|AI999923.1|AI999923
EST:     GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAG
genomic: GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAG
EST: gi|211229612|gb|FL380029.1|FL380029
EST:     GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
EST: gi|211212797|gb|FL419176.1|FL419176
EST:     GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAG                         GTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT
genomic: GGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccg ... cttgaaatagGTCTGGATGTGAAGAAGGTCGATAAATGCATGGGAGACCCAAATGCTGATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGTCTGGTGGGATTATGTGACTGATTTTCACATAAGGTGTCCAATGAAGGAGAAGAAGTACAATAAAAAATGTGCAGAAACTGTCATCAAATCACTAGgtttgctccgttttctttcctcgcttacttaagaatccacattgtatatatattttgtaaaaacatgtttgtaagtttttaacatgcttggcacccactt

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT