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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatttccgatattgcttttactttcattaggaaaaagcttgccttcagtgacttaacgatatcacagtattaaaatttataactttatgattca...

Basic information

species Zea mays
transcript GRMZM2G059671_T05
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059671_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g32610.4 (Oryza sativa), 5'ss of exon 12
GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatttccgatattgcttttactttcattaggaaaaagcttgccttca-gtgacttaacgatatcacagtattaaaatttataactttatgattca---
|| || |||||||| || ||||| ||||| |||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||||||||||||||| ||||    |||    ||    |||| |  |  ||    |   | |||  ||||  | |||    |   |     |  | |  |||   ||||| |  ||     
GCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAGgtatatccttt----tacccattttgccatattttaagacctgtttgatttcacattactctttgtggtactttttgttattttttctactttgtttttggaca

upper sequence: GRMZM2G059671_T04 (Zea mays), 5'ss of exon 11
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 5'ss of exon 11
GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatttccgatattgcttttactttcattaggaaaaagcttgcct------tcagtgacttaacgatatcacagtattaaaatttataactttatgattca---
|| || || ||||| ||||||||||| || |||||||| || || || || ||| | ||||| |||||||| |||||||||||||| ||||| ||||| ||| ||       |  ||  |||   ||| ||  ||  | | |  | | |      ||| ||   || |   | |  ||| ||      |   ||||| || ||     
GCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAGgtaagag-----tggaatatcttgagcttgca--agatagacgtctacttcgataatcaatgttctagc--caccttagttttgctgccttgcactttttgttttgatt
















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|20802940|gb|BQ293990.1|BQ293990
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|26456437|gb|CA828020.1|CA828020
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|20336958|gb|BQ172588.1|BQ172588
EST:     GGGATCTTGAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
EST: gi|60337361|gb|DN204334.1|DN204334
EST:     GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAA                         GTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC
genomic: GGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatt ... tattctgcagGTCTGTGACTTTGGTCTCTCCAGATTGAAGGCAAACACATTTCTGTCTTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAAGGGATGAACTATCTTCATAAGCGTAATCCTCCAATAGTCCACCGGGATCTTAAGTCACCAAACCTGTTGGTTGACAAAAAGTACACTGTGAAAgtatgaaatttccgatattgcttttactttcattaggaaaaagcttgccttcagtgacttaacgatatcacagtattaaaatttataactttatgattca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaaaa