Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgctgccgttgtcagaactcagaagcttgtatatgcggaaatctacttattattagttattaaatgctgctggcccctctggtgttgggacatggacgcag

Basic information

species Zea mays
transcript GRMZM2G180815_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g44394.1 (Oryza sativa), 5'ss of exon 2
GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgctgccgttgtcagaactcagaagcttgtatatgcggaaatctacttattattagttattaaatgctgctggcccctctggtgttgggacatggacgcag-----------------
|||| ||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||  |    |      |    ||| ||  | |  |      |   | || || |||    || ||   || | | |||   || | |  ||| |    ||    |                 
GTGAATCCGGCGCCCGGGGACTCGGTTTCCAGCCTCAGCTTCAGTCCCAAGGCGAACCACCTCGTCGCCACATCATGGGACAACCAGgtgagccccgcccgcccaccgtcgctc-gagccctagacgcttcgttttttattttttaaacatttttgtttgtttc-ggcgaatccgctagtggaatcctgagattgcggttggaattttgcag

upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 2
GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgctgccgttgtcagaactcagaagcttgtatatgcggaaatctacttattattagttattaaatgctgctggcccctctggtgttgggacatggacgcag
|||| || | | ||    || || |||||||| ||||||||||| ||||| || |||  |||||| ||||| || |||||||| |||||| |          ||      ||||   |  | |   ||    | ||   ||| | |  |  | ||      | |  |                            
GTGAATCAGCCTCCCACTGATTCCGTGTCCAGTCTCAGCTTCAGTCCCAAAGCCAACTTCCTCGTCGCCACTTCTTGGGACAATCAGgtgtgtctttctttctttctttcactctttacttcg---atagatagataggcttgtgagcaacttttc--cttttccag----------------------------

upper sequence: GRMZM2G180815_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S33_129V6.1 (Physcomitrella patens), 5'ss of exon 2
GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgctgccgttgtcagaactcagaagcttg---tatatgcggaaatctacttatt--attagttattaaatgctgctggcccctctggtgttgggacatggacgcag
|| | ||   | ||    ||     | || || ||   |||||| || ||||||||| | || ||||||||||||||||| || ||||||| | ||    | ||   |    |  || ||||    ||| |    ||||    |||||  |||  ||||||    |   |  |  |  |  |  ||              
GTCAATCAACCTCCAACTGATGGTATTTCGAGTCTTGCCTTCAGTCCAAAGGCGAACTATCTGGTTGCCACCTCATGGGATAATCAGgtgatg-cgtcatcctttctaaccgttcgatgctttcattatttttttaaattcttttattgcattgtttattagtctcccttaccgtcgttcctactgct------------

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|50331331|gb|CO526457.1|CO526457
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|211313573|gb|FL072330.1|FL072330
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|91878349|gb|EB408306.1|EB408306
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|71448754|gb|DR829804.1|DR829804
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|78073885|gb|DV502319.1|DV502319
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|74235195|gb|DT643109.1|DT643109
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|211313572|gb|FL072329.1|FL072329
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|88757960|gb|DY542101.1|DY542101
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|94472144|gb|EB701102.1|EB701102
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|211313574|gb|FL072331.1|FL072331
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|74234227|gb|DT642141.1|DT642141
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|71432894|gb|DR813944.1|DR813944
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|50332450|gb|CO527576.1|CO527576
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|74240564|gb|DT648478.1|DT648478
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
EST: gi|76930213|gb|DV172299.1|DV172299
EST:     GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAG                         GTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC
genomic: GCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCC

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: 47 (upstream exon), 49 (downstream exon)
Score: 120

GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 19

GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG


Block sizes: 41 (upstream exon), 38 (downstream exon)
Score: 14

GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG


Block sizes: 41 (upstream exon), 48 (downstream exon)
Score: 15

GTGACTCCGGCGCCTGGGGACTCGGTGTCCAGCCTCAGCTTCAGCCCCAAGGCGAACCACCTCGTTGCCACCTCATGGGACAACCAGgtgaggtcgc ... atggacgcagGTTCGGTGCTGGGAGGTCATGGCTGGTGGGGCCTGCCAAGCGAAGGCCTCCATTTCGCACGATCAACCG