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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_T07
intron # 13
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|15426921|gb|BI542743.1|BI542743
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|67023551|gb|CO452300.1|CO452300
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTCCAG                         GTCTCCANAGACGG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGG
EST: gi|5650248|gb|AI920608.1|AI920608
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|32833578|gb|CD973256.1|CD973256
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTCCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTAAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|78021110|gb|DV489497.1|DV489497
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|211335099|gb|FK972896.1|FK972896
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|32833853|gb|CD973531.1|CD973531
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTCCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTAAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|211409237|gb|FL441028.1|FL441028
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG
EST: gi|33091895|gb|CF051889.1|CF051889
EST:     AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTCCAG                         GTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTAAGGGAGCGGTTG
genomic: AGCTGATAACGAAACCGAATGCTGACGGCCACGTGAACAACTATGTTCAGgtgagatcct ... ttggctgcagGTCTCCAGAGACGGCACGAGCGATGAAGAGAAGGAGCTTAGGGAGCGGTTG

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