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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACTACCTGGAATATATCAAGAGAGAGAAGAATGGAGCTCTTCAGGCCTTTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgtatagcttagttgttttgttaattacacggatgcccatgaacactcctaatgttattcatctatag

Basic information

species Zea mays
transcript GRMZM2G092588_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092588_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g33580.1 (Oryza sativa), 5'ss of exon 5
AAACTACCTGGAATATATCAAGAGAGAGAAGAATGGAGCTCTTCAGGCCTTTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgtatagcttag-ttgttttgttaattacacggatgcccatgaacactcctaatgttattcatctatag---------
 || ||||| |||||||||||||||||||||||||| |||||||| || || || || ||||||||||||||||||||||||||||||||||| || ||||| || | | ||||| |  ||||| || || | |   |||||| | |   || |   | | ||  | ||  || |         
GAATTACCTAGAATATATCAAGAGAGAGAAGAATGGTGCTCTTCAAGCTTTCCTGGTCAAACACATCAACAATTGGGTGACCAGAGCATACTGCGATAAGgtgctgtatctagctcaacttgttctggta-tcatctggatgcactt---cagtttcagtattgctaatgaatggcttatgcag

upper sequence: GRMZM2G092588_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G36050.1 (Glycine max), 5'ss of exon 5
AAACTACCTGGAATATATCAAGAGAGAGAAGAATGGAGCTCTTCAGGCCTTTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtac-----tttgtatagcttagttgttttg---ttaattacacggatgcccatgaacactcctaatgttattcatctatag-------------------
||| ||  | |||||||||||||| ||||| ||||| || || ||||| || || || |||||||| ||||| ||||| || |||||||||||  ||||||||      ||| |  | | ||||    |||   | |  || | |       |  ||  ||  |   | |   | |||                       
AAATTATTTAGAATATATCAAGAGGGAGAAAAATGGGGCACTCCAGGCATTCCTGGTGAAACACATAAACAACTGGGTTACAAGAGCATACTGCCACAAGgtatgagaatttat-catcctagtaagcttggattaaggtagaagctaattgactaaacctttttgggcttcccttctccttaaaactagaagctccttca

upper sequence: GRMZM2G092588_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G11670.2 (Arabidopsis thaliana), 5'ss of exon 5
AAACTACCTGGAATATATCAAGAGAGAGAAGAATGGAGCTCTTCAGGCCTTTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgtatagcttagttgttttgttaattacacggatgcccatgaacactcctaat--gttattcatctatag----------------------------
||||||| | || || |||||||| |||||||||||||||||||| || ||| | || || ||  | ||||||||||| ||  |||| || |||||||||||   |  | || ||   ||  ||      ||   | | |||   ||||  ||| | |    | | |  |  |                               
AAACTACTTAGAGTACATCAAGAGGGAGAAGAATGGAGCTCTTCAAGCATTTTTTGTGAACCATGTAAACAATTGGGTCACACGAGCGTATTGTGACAAGgtgaatcatcta-ctctatttcttcaagccttgttctgttgct--tgaatcctctttactaataaatagtacacgagctaatacatattttctactcatgaaag

upper sequence: GRMZM2G092588_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0105g00260.t01 (Vitis vinifera), 5'ss of exon 5
AAACTACCTGGAATATATCAAGAGAGAGAAGAATGGAGCTCTTCAGGCCTTTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgta-ctttgtatagcttagttgttttgttaattacacggatgcccatgaacactcctaatgttattcatct-atag---------------------------
||| ||| | ||||||||||||||||||||||| || || || || || ||  | || |||||||| || ||||||||  | |||||||||||  |||||||| || | |||    |   | || ||   ||   | |  ||   |||  |  ||   || || |   | | ||||                           
AAATTACTTAGAATATATCAAGAGAGAGAAGAACGGGGCACTCCAAGCTTTCTTTGTGAAACACATAAATAATTGGGTTGCAAGAGCATACTGCCACAAGgtaactgtctattatgtgcatattctg---atctgatgattggtgatgttctttctccattttgtgtgttttatagcatggtctgtctgtaactagttcaata

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|71427681|gb|DR808731.1|DR808731
EST:     TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAG                         GTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
genomic: TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgta ... tcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
EST: gi|47961892|gb|CN844601.1|CN844601
EST:     TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGCGACAAG                         GTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
genomic: TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgta ... tcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
EST: gi|211377158|gb|FL183054.1|FL183054
EST:     TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGCGACAAG                         GTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC
genomic: TTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgta ... tcatctatagGTCTTACGTCTTTCTGCAGCAACTCAAGATTTACCAAAGTCTATTGTTTGC

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACTACCTGGAATATATCAAGAGAGAGAAGAATGGAGCTCTTCAGGCCTTTCTAGTTAAACACATCAACAATTGGGTGACCAGAGCATACTGTGACAAGgtactttgtatagcttagttgttttgttaattacacggatgcccatgaacactcctaatgttattcatctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA