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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGGAGGATGGCTGCAGCCGCGGGGAGGAAGGTGGCGGTCGCCGCCGTGCAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctattgcccgcccgcctgcccgcctacatccctaagttaacaccgcacctgattccctctccccccgagaagccgaactcctagccgttcagtct...

Basic information

species Zea mays
transcript GRMZM2G073950_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G073950_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 5'ss of exon 1
AGAGGAGGATGGCTGCAGCCGCGGGGAGGAAGGTGGCGGTCGCCGCCGTGCAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctattgcccgcccgcctgcccgcctacatccctaagttaacaccgcacctgattccctctccccccgagaagccgaactcctagccgttcagtct-
||| |  |  ||  |  | ||||||||| |||||| |||||||||||||||||||||||||||||||||||||| | |||||||||| |||||| ||||||| || | |       ||     |||| |  | ||||   |    | || | ||     ||| |        ||  |  ||   ||  |  |    |    
AGATGGCGGGGGGCGGGGGCGCGGGGAGTAAGGTGTCGGTCGCCGCCGTGCAGTTCGCCTGCACCGACGTCGAGTCCGAGAACGTCGACACCGCGGAGAGgtatgttgtccggtatccctaaccccgtccccgtccccccgcccccccccccccccccccccccaaattgt-aggggtagattgccccgaaggaaggaacc
















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|211074743|gb|FL419972.1|FL419972
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|211141684|gb|FL053512.1|FL053512
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|91056600|gb|EB167018.1|EB167018
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|148953399|gb|EE152896.2|EE152896
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|78081735|gb|DV510147.1|DV510147
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|88758160|gb|DY542301.1|DY542301
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|50324199|gb|CO519325.1|CO519325
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGACTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|148939361|gb|EC883888.2|EC883888
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|78078908|gb|DV507320.1|DV507320
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|29167916|gb|CB411176.1|CB411176
EST:     ACGTCGCCACCGCCGAGAG                         G-TGATTAGAGAAGCACACAAGAAAGG-GCAAAGA-TGTACTCGTTCAG
genomic: ACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|71417127|gb|DR803933.1|DR803933
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|211482279|gb|FL401962.1|FL401962
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|94478259|gb|EB707217.1|EB707217
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
EST: gi|78077686|gb|DV506120.1|DV506120
EST:     CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCCCCGCCGAGAG                         GTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG
genomic: CAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 159

AGAGGAGGATGGCTGCAGCCGCGGGGAGGAAGGTGGCGGTCGCCGCCGTGCAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

AGAGGAGGATGGCTGCAGCCGCGGGGAGGAAGGTGGCGGTCGCCGCCGTGCAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 188

AGAGGAGGATGGCTGCAGCCGCGGGGAGGAAGGTGGCGGTCGCCGCCGTGCAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 188

AGAGGAGGATGGCTGCAGCCGCGGGGAGGAAGGTGGCGGTCGCCGCCGTGCAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctatt ... tgttttacagGTTGATTAGAGAAGCACACAAGAAAGGTGCAAAGATTGTACTCGTTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGGAGGATGGCTGCAGCCGCGGGGAGGAAGGTGGCGGTCGCCGCCGTGCAGTTCGCCTGCACCGACGTCGAGGCGGAGAACGTCGCCACCGCCGAGAGgtttgctattgcccgcccgcctgcccgcctacatccctaagttaacaccgcacctgattccctctccccccgagaagccgaactcctagccgttcagtct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgcacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccc