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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgctactgaactgagttcctatctattttcctgtatccgcaagttgagtattgtgaatgctgcattattgttattggcgagcagaattggacaa...

Basic information

species Zea mays
transcript GRMZM5G818887_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 5'ss of exon 2
GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgctactgaactgagttcctatctattttcctgtatccgcaagttgagtattgtgaatgctg-cattattgttattggcgagcagaattggacaa-
||| ||||||||||| |||||||||||||||||||||||  || | ||||| |||||||||||| | || ||||||||| | || || || ||||   |  || ||    ||        | || |  ||     | || ||| |||||||| |         | ||| |   
GGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCTCCCGACAAGCAATTCCTCGTCACCAGGAACGgtatgctgattctaaattg-gttctatttcatcttgtgctaggattcgatggaatgctgcattgggtgacatgattgttat-gctagtttccactggtcttg

upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 2
GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgctactgaactgagttcctatctattttcctgtatccgc--aagttgagtattgtgaatgctg-cattattgttattggcgagcagaattggacaa
||| ||||||||||| |||||||||||||||||||||||  |  | ||||| || ||||||||| | || ||||||||| | ||| | ||   | |||| |  | |  |  || ||    | | || |  ||     | || ||| ||||||||           | |    | 
GGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCACCTGACAAGCAATTTCTCGTCACCAGGAACGgtatgctgattctggattg--cttctatttcatcttgtacatgcgatggaatggaatgctgcattgggtggcatgattgttatgcttagtttccacttccta-
















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|148960724|gb|EE011368.2|EE011368
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|78091451|gb|DV519825.1|DV519825
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|149045355|gb|EE047779.2|EE047779
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|76013821|gb|DT940991.1|DT940991
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|71313249|gb|DR793148.1|DR793148
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|87156323|gb|DY401112.1|DY401112
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211324976|gb|FL012745.1|FL012745
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGGCCTGGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCA
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTG-TTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCA
EST: gi|78113031|gb|DV531425.1|DV531425
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|76016277|gb|DT943447.1|DT943447
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG

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: 48 (upstream exon), 48 (downstream exon)
Score: 82

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 211

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 162

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACA