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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcctcctgtcccgtcaaatggatgccatagctgagggctgagagtgcacgcgtttttcttggctgcag

Basic information

species Zea mays
transcript GRMZM2G052546_T05
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052546_T05 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g01750.7 (Oryza sativa), 5'ss of exon 12
GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagat-cctcctgtcccgtcaaatggatg---ccatagctgag--ggctgagagtgcacgcgtt--tttcttggctgcag
|||||||||||||||  ||||||| ||||||||| | ||||| ||  |||||  ||  || ||| | |||||||| ||||| ||||| ||||| || |||||||| | | |||   | |   |  |   ||   |  | |  | |  || |  ||   |     ||    ||||   |||||
GTATGAATACAAATATATAGTGGACGGCAAATGGGTGTGCAATGACAATGAGAAGAAGACCAAAGCAAATGCTGATGGCCATGTGAATAACTACGTCCAGgtgagttacttcccagctccctagttccctgtatctgtggacgtgttggataggataacgtaacttgacgtcttcattgcag
















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|211496893|gb|FL296175.1|FL296175
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAG-AGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|211496895|gb|FL296177.1|FL296177
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|211300578|gb|FL480031.1|FL480031
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|211496894|gb|FL296176.1|FL296176
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|211122780|gb|FL444953.1|FL444953
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG

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: 249

GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTGACTGGTCCGGACCCTGATCTCACGGACCAGGAGAGGCTGATGATCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 347

GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTGACTGGTCCGGACCCTGATCTCACGGACCAGGAGAGGCTGATGATCAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTGACTGGTCCGGACCCTGATCTCACGGACCAGGAGAGGCTGATGATCAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 476

GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTGACTGGTCCGGACCCTGATCTCACGGACCAGGAGAGGCTGATGATCAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGAATACAAATACGTAGTGGATGGCAAATGGCTATGCAACGAGCATGAGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcctcctgtcccgtcaaatggatgccatagctgagggctgagagtgcacgcgtttttcttggctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG