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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAGCTACTGGGAGTCTATGAAGTCTGGCGTGGCTGATATGGTCAACACTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttctgtttgtttttttcttttcttttgacacgcctaaatacattatgaaatttgatcacagcgataggaccattggagtggtgagagattaagaatccgccacgatagtgaacactttgacaggacagacttccagagcagtggtaacggcatgaacgccgcttttgtgtccctcccttgttgcag

Basic information

species Zea mays
transcript GRMZM2G178958_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178958_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os02g55140.1 (Oryza sativa), 5'ss of exon 8
AGAGAGCTACTGGGAGTCTATGAAGTCTGGCGTGGCTGATATGGTCAACACTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttctgtttgtttttttcttttcttttgacacgcctaaatacattatgaaatttgatcacagcgataggaccattggagtggtgagagattaagaatccgccacgatagtgaacactttgacaggacagacttccagagcagtggtaacggcatgaacgccgcttttgtgtccctcccttgttgcag
 || |||||||||||||| ||||||||||| || ||||| ||||| ||||| || ||| ||||||| ||||||||||| || || || ||||||||||||||| ||||           ||| || |   |  |       ||  | |  |   |     ||      | ||||  |||| || |    | || |  |      | || | || || |  ||    |  |    | || |||                                                  
GGAAAGCTACTGGGAGTCGATGAAGTCTGGTGTTGCTGACATGGTTAACACCGGTGGCCGGCAGGGTGGTTCTATTACTGCTGCACTCTTCCTGAAACAGgtaaattt------accactttattatgaatgaa---attcaagcaaaacacacagccacatgctctaggtaggcacatttgaat----aaagttgtaagcagtgacatgctaatggagcctcatgcttgt---atttgcag--------------------------------------------------

upper sequence: GRMZM2G178958_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT2G24200.2 (Arabidopsis thaliana), 5'ss of exon 10
AGAGAGCTACTGGGAGTCTATGAAGTCTGGCGTGGCTGATATGGTCAACACTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttctgtttgtttttttcttttcttttgacacgcctaaatacattatgaaatttgatcacagcgataggaccattggagtggtgagagattaagaatccgccacgatagtgaacactttgacaggacagacttccagagcagtggtaacggcatgaacgccgcttttgtgtccctcccttgttgcag
||||||||| ||||||   ||||||||||| |||||||||||||||||||| |||||  ||   ||||| || || ||||| || || ||| ||||||||||  |       |              |||| ||  |   || ||||||  |    |||||      | | |    | | ||     ||| ||      || |  || | ||  |      | || |||                                                               
AGAGAGCTATTGGGAGATGATGAAGTCTGGAGTGGCTGATATGGTCAACACAGGCGGGCGGGCAGGAGGATCCATCACCGCGGCTCTCTTCTTGAAACAGgtgaaaacaaagtc------------cctttagaggc-tatacatacatgtt----tttga------caaaaaattcgtcgg-----tgaaagtaactaaaccatcctctattttctgtggtatggcag---------------------------------------------------------------

upper sequence: GRMZM2G178958_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 5'ss of exon 9
AGAGAGCTACTGGGAGTCTATGAAGTCTGGCGTGGCTGATATGGTCAACACTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgta--catttctgtttgtttttttcttttcttttgacacgcctaaatacat-tatgaaatttg---atcacagcgataggaccattggagtggtgagagattaagaatccgccacgatagtgaacactttgacaggacagacttccagagcagtggtaacggcatgaacgccgcttttgtgtccctcccttgttgcag
 ||||| || |||||||| ||||| || || || |||||||||||||||||||| ||| | |  || ||| |||| || || || |||||| |||||||||||  |   |||| |  || | |  | || |||| |      |   | | |  ||| | ||||   || |   | |  || |||    | | |  || || ||                                                                                               
GGAGAGTTATTGGGAGTCCATGAAATCAGGAGTAGCTGATATGGTCAACACTGGTGGCCGTCCAGGTGGTGCTATCACTGCAGCTCTGTTCTTGAAACAGgtaagcggatctgatcattctctcttattgttttaaatgttttcccttcttacatggagtttgtatatgatttccactggcccac---aattggcagtgaata-----------------------------------------------------------------------------------------------

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|76291679|gb|DV031247.1|DV031247
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|71435918|gb|DR816968.1|DR816968
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|18179365|gb|BM380575.1|BM380575
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|211464859|gb|FL438563.1|FL438563
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|71762466|gb|DR960403.1|DR960403
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|149026811|gb|EE046171.2|EE046171
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|78121906|gb|DV540290.1|DV540290
EST:     CCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|211121581|gb|FL034200.1|FL034200
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|71770054|gb|DR967991.1|DR967991
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|148936676|gb|EC880804.2|EC880804
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|148948295|gb|EC893812.2|EC893812
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|71431472|gb|DR812522.1|DR812522
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|71431471|gb|DR812521.1|DR812521
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|211513614|gb|FL043450.1|FL043450
EST:     TCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: TCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|84969659|gb|DW468088.1|DW468088
EST:     GGAGGTTTTATTTCCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: GGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|110970954|gb|EE190854.1|EE190854
EST:     CTGGCGGCAGGCAGGGAGGTTTTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|21843359|gb|BQ703940.1|BQ703940
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|32913173|gb|CF017985.1|CF017985
EST:     TATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: TATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|32907149|gb|CF011962.1|CF011962
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|76016701|gb|DT943871.1|DT943871
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
EST: gi|74234445|gb|DT642359.1|DT642359
EST:     CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAG                         TTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG
genomic: CTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttct ... cttgttgcagTTCGTCGACGACAAGGTCCAGTGGATGCACATCGACATGGCCGGGCCAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAGCTACTGGGAGTCTATGAAGTCTGGCGTGGCTGATATGGTCAACACTGGCGGCAGGCAGGGAGGTTCTATTACCGCCGCGCTGTTCCTGAAACAGgtacatttctgtttgtttttttcttttcttttgacacgcctaaatacattatgaaatttgatcacagcgataggaccattggagtggtgagagattaagaatccgccacgatagtgaacactttgacaggacagacttccagagcagtggtaacggcatgaacgccgcttttgtgtccctcccttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT