Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttataattgatgtcatatctagctataatagaccaccactcatagaacatcactgtatcgatcctcatgttcccaacgcggacgtgactgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA

Basic information

species Zea mays
transcript GRMZM2G059845_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059845_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g10080.2 (Oryza sativa), 3'ss of exon 1
tcttataattgatgtcatatctagctataatagaccaccactcatagaacatca-ctgtatcgatcctcatgttcccaac--gcggacgtgactgaatttcagGAAGTGC---CGGCGACGTGCTGGAG--GACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA---------------------
                             | ||| |||       |     | | ||  ||  ||  | |  ||||   |  |||||  ||| | || |||| |||||||    || || ||||| |||  ||||| || || ||   ||| |||||||| || |||||||||||||||||||||||||||||| | |||||||| ||                     
-----------------------------aaagaacactttcagcaatgttttaactccatttatattaactttccttgctcgcggatatgattaaaattcacgaagtgctgctggtgatgtgctagagAAGACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGTACAACAAGAACATTGTGGCGAAAGATTCCAGATGCCTCAGCCACAT

upper sequence: GRMZM2G059845_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g10080.3 (Oryza sativa), 3'ss of exon 1
tcttataattgatgtcatatctagctataatagaccaccactcatagaacatca-ctgtatcgatcctcatgttcccaac--gcggacgtgactgaatttcagGAAGTGCC---GGCGACGTGCTGGAG--GACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA-------------------
                            || ||| |||       |     | | ||  ||  ||  | |  ||||   |  |||||  ||| | || |||| |||||||    || || ||||| |||  ||||| || || ||   ||| |||||||| || |||||||||||||||||||||||||||||| | |||||||| ||                   
---------------------------aaaaagaacactttcagcaatgttttaactccatttatattaactttccttgctcgcggatatgattaaaattcacgaagtgctgctggtgatgtgctagAGAAGACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGTACAACAAGAACATTGTGGCGAAAGATTCCAGATGCCTCAGCCAC

upper sequence: GRMZM2G059845_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g10080.1 (Oryza sativa), 3'ss of exon 1
tcttataattgatgtcatatctagctataatagaccaccactcatagaacatca-ctgtatcgatcctcatgttcccaac--gcggacgtgactgaatttcagGAAGTGC---CGGCGACGTGCTGGAG--GACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA------------------------
                                || |||       |     | | ||  ||  ||  | |  ||||   |  |||||  ||| | || |||| |||||||    || || ||||| |||  ||||| || || ||   ||| |||||||| || |||||||||||||||||||||||||||||| | |||||||| ||                        
--------------------------------gaacactttcagcaatgttttaactccatttatattaactttccttgctcgcggatatgattaaaattcacgaagtgctgctggtgatgtgctagagaagACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGTACAACAAGAACATTGTGGCGAAAGATTCCAGATGCCTCAGCCACATGTT

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|91876290|gb|EB406247.1|EB406247
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|91876209|gb|EB406166.1|EB406166
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|88756465|gb|DY540606.1|DY540606
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|211215553|gb|FL199928.1|FL199928
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|76011529|gb|DT938699.1|DT938699
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|211215552|gb|FL199927.1|FL199927
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|50337832|gb|CO532958.1|CO532958
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|149099210|gb|EE185237.2|EE185237
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|78114761|gb|DV533149.1|DV533149
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|71434936|gb|DR815986.1|DR815986
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|94479511|gb|EB708469.1|EB708469
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|88753209|gb|DY537350.1|DY537350
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|78074303|gb|DV502737.1|DV502737
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|148944961|gb|EC890130.2|EC890130
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|101402183|gb|EB822688.1|EB822688
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|71432339|gb|DR813389.1|DR813389
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|89251212|gb|DY622998.1|DY622998
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|91050847|gb|EB161265.1|EB161265
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|93284342|gb|EB676606.1|EB676606
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
EST: gi|71313729|gb|DR793454.1|DR793454
EST:     CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAG                         GAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT
genomic: CTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGT

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: 41 (upstream exon), 48 (downstream exon)
Score: 33

GGGAGCGCGACGGCGGCGCAGGCCCTGGCGCTCGCCGCCTTGCTCCTCGCCTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 78

GGGAGCGCGACGGCGGCGCAGGCCCTGGCGCTCGCCGCCTTGCTCCTCGCCTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 115

GGGAGCGCGACGGCGGCGCAGGCCCTGGCGCTCGCCGCCTTGCTCCTCGCCTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 144

GGGAGCGCGACGGCGGCGCAGGCCCTGGCGCTCGCCGCCTTGCTCCTCGCCTGCTCCGGCGTCGCCGTCGTCACGGCGCAGGACATCGAGCGGATCCAAGgtactacgcg ... tgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacatcactgtatcgatcctcatgttcccaacgcggacgtgactgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA
                                             tgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttataattgatgtcatatctagctataatagaccaccactcatagaacatcactgtatcgatcctcatgttcccaacgcggacgtgactgaatttcagGAAGTGCCGGCGACGTGCTGGAGGACGACCCCGTCGGGCGGCTCAAGGTGTACGTGTACGAGCTGCCCCCCAAGTACAACAAGAACGTGGTGGCGAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - -attgatg
- - - - - - - - - - - - - - - - - -caccact
- - - - - - - - - - - - - - - - - - - - - - - -aacatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtatc