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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttccataccaatgcaagtctgaacatcaatgctgtgaggtctggtcgatatcttgtcttactaatccttgtttgtag

Basic information

species Zea mays
transcript GRMZM2G063792_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063792_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os12g27520.1 (Oryza sativa), 5'ss of exon 10
GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgtt------------ccataccaatgcaagtctgaacatcaatgctgtgaggtctggtcgatatcttgt-cttactaatc-cttgtttgtag
|| || || || || ||||| || ||||||||||| ||||| |||||||||||||| ||  |||| |||||||| |  || ||||| || |||||||||||||||            || |  || ||  |||  | |  |||  ||  || ||  | || | |||  ||| || | |  |  ||||| |||||
GGAGAAGCATTGTTTCAGACCCATGAAAACTTGGAGCATCTTGCTATGATGGAGAGGGTATTTGGTCCTTTGCCATGTCACATGCTCAAAAGGGCAGAgtatgttgctgtccttgatccgtctcattgtcagtaagcat-tcacagcattggggattagtaggtattgtgtgctcatttgttgcttgtatgtag

upper sequence: GRMZM2G063792_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA04G36360.1 (Glycine max), 5'ss of exon 9
GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttccataccaatgcaagtctgaacatcaatgctgtgaggtctggtcgatatcttgtcttactaatccttgtttgtag--------------------
||||| || || || |||||||| ||||| || || |||||||||||||||||||| || ||||| ||| | ||  | || ||| | ||||| |  ||||| ||    ||||  ||  | | |       | |  | | |  | |     ||   |   |||    ||    |  ||||                     
GGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTGGCTATGATGGAGAGGGTGCTTGGTCCTATACCACAGCAGATGTTAAAGAGAGTTGAgtaagtgatttacct-tgtgaatttt----ctattattatcaaatttatcaaatgattgaacttgaacataaccgagtgtatcttttactctgcccatgtag
















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|7145535|gb|AW507016.1|AW507016
EST:     ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttcca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|211114732|gb|FL311570.1|FL311570
EST:     ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttcca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|166420121|gb|EG323903.1|EG323903
EST:     AGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: AGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttcca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|71446077|gb|DR827127.1|DR827127
EST:     ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttcca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|60398865|gb|DN231681.1|DN231681
EST:     ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttcca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
EST: gi|211367186|gb|FL433650.1|FL433650
EST:     ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGA                         TCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG
genomic: ATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttcca ... ttgtttgtagTCGGCACTCTGACAAATACATCAGAAAAGGACGCCTGAATTGGCCTGAGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGAGGCGTTATTCCAGACTCACGAAAACTTGGAACATCTGGCTATGATGGAGAGAGTTCTTGGACCTTTGCCGTACCATATGCTTAAGAGGGCAGAgtatgttccataccaatgcaagtctgaacatcaatgctgtgaggtctggtcgatatcttgtcttactaatccttgtttgtag

- - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG