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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacaatcttgttctcctatgcacagaaattggcatttaatctattcatttctgagtgatttattttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG

Basic information

species Zea mays
transcript GRMZM2G095969_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g06440.1 (Oryza sativa), 3'ss of exon 7
gtatacaatcttgttctcctatgcacagaaattggcatttaatc-tattcatttctgagtgattt-attttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG
||||||  ||   |   |  ||   |  | | ||  | ||| ||  ||   ||||||||  |||| ||  ||| ||||||||||| |||| |||||||| |||||||||||||||||| |||| ||||||||||||||||| ||||||||||||||||||||||| ||  || ||   
gtatactctcacataaacacat---cgaataatgatagttattcacatatttttctgagcaattttatactgt-ttagGTACTTCAAGAAGCAATTTGAATTGGCTGAAGCAGTAAAATTGCCAATGTTTCTTCACATGCGGGCTGCTGGTGAAGACTTCTGTGAGATTGTGTCAGAA

upper sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g06410.5 (Oryza sativa), 3'ss of exon 5
gtatacaatcttgttctcctatgcacagaaattggcatttaatctattcatttctgagtgatttattttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG
   || | |||    |    |    |  | | ||  | ||| ||   |  ||||||||  ||||  |     ||||||||||| |||| |||||||| ||||||||||||||||||||||| ||||||||||||||| | ||||||||||||||||||||||| ||  |  ||   
--gtatagtctcacacaagcacat-cgaagaatgatagttattcgcatattttctgagcaattttgtgctgtttagGTACTTCAAGAAGCAATTTGAATTGGCTGAAGCAGTAAAACTGCCAATGTTTCTTCACATGAGGGCTGCTGGTGAAGACTTCTGTGAGATTGTATCAGAA
















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|101392457|gb|EB818158.1|EB818158
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|88757501|gb|DY541642.1|DY541642
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|76936926|gb|DV174965.1|DV174965
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211481566|gb|FL145739.1|FL145739
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTTGAGAAACAATTTGAGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTT
EST: gi|78179334|gb|DV549707.1|DV549707
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211484447|gb|FL145748.1|FL145748
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|7009462|gb|AW455727.1|AW455727
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211487326|gb|FL145759.1|FL145759
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGT
EST: gi|211487336|gb|FL145769.1|FL145769
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTT
EST: gi|94477631|gb|EB706589.1|EB706589
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211487328|gb|FL145761.1|FL145761
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTTGAGAAACAATTTGAGTTGGCTGAAGCGGTAAAACTGC
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGC
EST: gi|71774366|gb|DR972244.1|DR972244
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATACGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|76021692|gb|DT948862.1|DT948862
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|74242558|gb|DT650472.1|DT650472
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|71434563|gb|DR815613.1|DR815613
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211487335|gb|FL145768.1|FL145768
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTTGAGAAACAATTTGAGTTGGCTGAAGCGGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211484453|gb|FL145754.1|FL145754
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTTGAGAAACAATTTGAGTTGGCTGAAGCGGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211481559|gb|FL145732.1|FL145732
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTANTTTGAGAAACAATTTGAGTTGG
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGG
EST: gi|89251475|gb|DY623261.1|DY623261
EST:     GGTTTGGATTATGACAGATTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211481563|gb|FL145736.1|FL145736
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTANAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|78108903|gb|DV527320.1|DV527320
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|37421738|gb|CF648570.1|CF648570
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|211481565|gb|FL145738.1|FL145738
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAA
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAA
EST: gi|71325561|gb|DR799471.1|DR799471
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
EST: gi|87157799|gb|DY402588.1|DY402588
EST:     GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA                         GTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT
genomic: GGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAAgtatacaatc ... tttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacagaaattggcatttaatctattcatttctgagtgatttattttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG
               atttaat  putative branch site (score: 4)
                                        tttatttt  putative PPT
               atttaatctattcatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacaatcttgttctcctatgcacagaaattggcatttaatctattcatttctgagtgatttattttgtattagGTACTTCGAGAAACAATTTGAGTTGGCTGAAGCAGTAAAACTGCCCATGTTTCTTCACATGCGTGCTGCTGGTGAAGACTTCTGTGAAATCATGACACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA