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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgctactgaactgagttcctatctattttcctgtatccgcaagttgagtattgtgaatgctgcattattgttattggcgagtagaattggacaa...

Basic information

species Zea mays
transcript GRMZM2G063355_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063355_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 5'ss of exon 2
GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgctactgaactgagttcctatctattttcctgtatccgcaagttgagtattgtgaatgctg-cattattgttattggcgagtagaattggacaa-
||| ||||||||||| |||||||||||||||||||||||  || | ||||| |||||||||||| | || ||||||||| | || || || ||||   |  || ||    ||        | || |  ||     | || ||| |||||||| |     |   | ||| |   
GGAGGCGGGCGATCCGAGCAAGAGGAAGCCGTATCTCCCTCCCGACAAGCAATTCCTCGTCACCAGGAACGgtatgctgattctaaattg-gttctatttcatcttgtgctaggattcgatggaatgctgcattgggtgacatgattgttat-gctagtttccactggtcttg

upper sequence: GRMZM2G063355_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 2
GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgctactgaactgagttcctatctattttcctgtatccgc--aagttgagtattgtgaatgctg-cattattgttattggcgagtagaattggacaa
||| ||||||||||| |||||||||||||||||||||||  |  | ||||| || ||||||||| | || ||||||||| | ||| | ||   | |||| |  | |  |  || ||    | | || |  ||     | || ||| ||||||||       |   | |    | 
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|211036315|gb|FL466133.1|FL466133
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCGTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|33770858|gb|CF273152.1|CF273152
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211327140|gb|FL012759.1|FL012759
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211327148|gb|FL012767.1|FL012767
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211324977|gb|FL012746.1|FL012746
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211329311|gb|FL012773.1|FL012773
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTCTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211327149|gb|FL012768.1|FL012768
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211327147|gb|FL012766.1|FL012766
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|148971664|gb|EE022387.2|EE022387
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|26559206|gb|CA831441.1|CA831441
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|15208976|gb|BI430860.1|BI430860
EST:     GAGGAAGCCGAATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211329317|gb|FL012779.1|FL012779
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211324974|gb|FL012743.1|FL012743
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211324988|gb|FL012757.1|FL012757
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|50331765|gb|CO526891.1|CO526891
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211327141|gb|FL012760.1|FL012760
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|22542051|gb|BU092489.1|BU092489
EST:     GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCTTAATG                         TGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
genomic: GAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAG
EST: gi|211327145|gb|FL012764.1|FL012764
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: 49 (upstream exon), 48 (downstream exon)
Score: 211

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACA


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

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACA


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

GGAAGCGGGCGATCCAAGCAAGAGGAAGCCGTATCTCCCCGCCAATAAGCAGTTCCTCGTCACCCGTAATGgtatgctgct ... ttactcccagTGCCCTGTTTAAGACGTGCCATCTCGGTTGAGGAAGAGTATGATGCAGCAGGAGCAGAGGTGGTTCTCGATGAGGATGGCGAAGGCTGGCTTGCAACACA