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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGCCACCGCTGGGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatgattgctttgaccgcgcagcagtatctgtgctgtgggctcacactcctctgaattgtgtcaactgatgcctgaacatttatttaacaagccatttacccctctttcccaactactgtcag

Basic information

species Zea mays
transcript GRMZM2G037923_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037923_T02 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 5'ss of exon 15
CAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGCCACCGCTGGGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatgattgctttgaccgcgcagcagt--atctgtg---ctgtgggctcacactcctctga--attgtgtcaactgatgcctga-acatttatttaacaagccatttacccctctttcccaactactgtcag
|||||| |||||||||||||| || ||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||| ||||| | ||||   |||||||| || |||||||   |        | |   ||        ||     | | | |||| |||  |||   | |  |  ||    | | || || |||  ||||    || || | ||  |   |   | | ||
CAATAAAAAGTGGAAAGAAGGTTTTCATGTGACATCTATGGCCACCGCTGGAAATCGCTGGGGTGTAGTTATGTCAAGGAACTCAGGTTACTCTGAACAGgttagaataattgcttgacctagttcatattcagtccacaaatttggcaatttatattcctgtgagcattccattatttactgtagaatatatctacttatgaagc----taacctttttctcatgccctttttag

upper sequence: GRMZM2G037923_T02 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 15
CAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGCCACCGCTGGGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatgattgctttgaccgcgcagcagtatctgtgc-tgtgggctcacactcctctgaattgtgtcaactgatgcctgaacatttatttaacaagccatttacccctctttcccaactactgtcag
 || ||||||||||||||||| |||||||| || || ||| | || ||||| | ||||||||| || || ||||| |||||| | ||||  |||  ||||||    ||   |  ||| |||    |    |   | ||  ||     | | | ||| |    |||  |    |  ||  |||  ||  |                                        
AAACAAGAAGTGGAAAGAAGGATTCCATGTTACCTCAATGACTACTGCTGGCAGTCGCTGGGGTGTTGTTATGTCCAGGAATGCTGGGTATTCTGATCAGgtatctatatct--tttcacctttgatttttggttatgtatgaatttttaaaatccacattgttgaatttgtttttgtttgatgatgcaag--------------------------------------

upper sequence: GRMZM2G037923_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 5'ss of exon 15
CAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGCCACCGCTGGGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatgattgctttgaccgcgcagcagtatctgtgctgtgggctc--acactcctctgaattgtgtcaactgatgcctgaacatttatttaacaagccatttacccctctttcccaactactgtcag
 || ||||| ||||||||||  |||||||| || |||||| | || ||||||||||| ||||| || || ||||| |||||||| || | ||||  ||||||  |  | | | |  | |||    |     ||      |      |   ||| |  ||   ||  | |    || |          || | | | |||                               
AAACAAGAAATGGAAAGAAGATTTCCATGTAACCTCCATGACAACTGCTGGGAATCGTTGGGGTGTGGTAATGTCGAGGAATTCTGGCTACTCTGATCAGgtaggtttcaatcccgtcaccttagaatgacataatctttaaacattttgacatttttcctgatactcttggttggta---------ttgtgtgaaaag-------------------------------

upper sequence: GRMZM2G037923_T02 (Zea mays), 5'ss of exon 15
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 5'ss of exon 15
CAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGCCACCGCTGGGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatgattgctttgaccgcgcagcagtatctgtgctgtgggctcacactc--ctctgaattgtgtcaactgatgcctgaacatt-tatttaacaagccatttacccctctttcccaactactgtcag
 ||||| |||||||||||||| || ||||| ||||||||| |||||||||||| ||| ||||| ||||| ||||| ||||| ||||| | ||||   ||||||     |||  ||||  | | |       | || | || ||    |    |   | ||  | ||| | ||| || |  |      | ||| | | |                                 
AAATAAAAAGTGGAAAGAAGGTTTTCATGTAACATCCATGACCACCGCTGGGAGTCGTTGGGGTGTAGTAATGTCCAGGAACTCAGGCTACTCTGAACAGgtt---ccgatctctttacctgaggcatttcaacttttctttgtttcctttttgagcactataatgtattaac-gaggtttatgtggtgtatattatag--------------------------------

upper sequence: GRMZM2G037923_T02 (Zea mays), 5'ss of exon 15
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 15
CAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGCCACCGCTGGGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatgattgctttgaccgcgcagcagtatctgtgctgtgggctcacactcctctgaattgtgtcaactgatgcctgaacatttatttaacaagccatttacccctctttcccaactactgtcag
 |||||||||||||||||||| |||||||| ||||| ||| | || ||||| | ||||||||| || || ||||| ||||| || || |   ||  ||||||||  || | |  |||        |  | | |     || | |  | |   |      ||||   |  |    |  ||||  ||||||||  |   |  |||||   | || |  |   |  |    
TAATAAGAAGTGGAAAGAAGGTTTCCATGTCACATCTATGACTACTGCTGGAAGTCGCTGGGGGGTGGTAATGTCCAGGAACTCTGGATATACTGATCAGgttacaattaatatttt--------attatttttctcactttag--taaatgtatgaacaatttcttttagaagtagctga-tatttatttccc---ctttttactggtgttgctgatacaaag----

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|21760105|gb|BQ635646.1|BQ635646
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|78023792|gb|DV492179.1|DV492179
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|21432270|gb|BQ547760.1|BQ547760
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|22473314|gb|BU037794.1|BU037794
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|211493560|gb|FL280135.1|FL280135
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|101385454|gb|EB814773.1|EB814773
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|33096596|gb|CF056590.1|CF056590
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|211124333|gb|FL444269.1|FL444269
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|22713641|gb|BU197414.1|BU197414
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|211490684|gb|FL280131.1|FL280131
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|22545509|gb|BU097868.1|BU097868
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|24770058|gb|CA405187.1|CA405187
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|61118390|gb|DN559351.1|DN559351
EST:     AGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: AGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|32858553|gb|CD998234.1|CD998234
EST:     AAGGAATTCCGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: AAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|31355521|gb|CD439878.1|CD439878
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|211490681|gb|FL280128.1|FL280128
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|21987385|gb|BQ778913.1|BQ778913
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|87156443|gb|DY401232.1|DY401232
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAT                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|78083128|gb|DV511521.1|DV511521
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|26559413|gb|CA831648.1|CA831648
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|67012040|gb|CO440789.1|CO440789
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|31356845|gb|CD441202.1|CD441202
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|148933318|gb|EC876975.2|EC876975
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
EST: gi|31350536|gb|CD434893.1|CD434893
EST:     GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAG                         GTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG
genomic: GGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatga ... ctactgtcagGTTGTAGAGTTGGATTTCCTGTACCCCAGCGAGGGCATCCACCGGCGCTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATAAGAAGTGGAAAGAAGGGTTCCATGTGACATCCATGGCCACCGCTGGGAATCGCTGGGGCGTAGTCATGTCAAGGAATTCAGGGTTCTCTACTCAGgttaggatgattgctttgaccgcgcagcagtatctgtgctgtgggctcacactcctctgaattgtgtcaactgatgcctgaacatttatttaacaagccatttacccctctttcccaactactgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA