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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtccagcttctgttgttccctgtgtatgttcatgttaaactctcaattccaacatgttgtttgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACTAAG

Basic information

species Zea mays
transcript GRMZM2G121223_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121223_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g08760.2 (Oryza sativa), 3'ss of exon 2
--------gtttgtccagcttctgttgttccctgtgtatgttc--------atgttaaactct-caattccaacatgttgtttgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACTAAG
          ||| || || | | |  |  |  |  |||   |        || || ||   |  |||| |||||||||| |||||||  ||||||| |||||||||||||||||||||||||| |||||  | || ||||||||||||||||| ||||||||||||||||| |||
gtatgacaacttgacctgcatatctcttgacaagcatatcccccaaattacatattgaatcatgtaatttcaacatgttgcttgttttgtagTTCCCTTTCTTTTGCAGTGACCGTGAATACATTTTTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG
















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|32799074|gb|CD951310.1|CD951310
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCGTTCTTTTGCGGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|148963895|gb|EE015006.2|EE015006
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCGTTCTTTTGCAGTGACCGTGA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCGTTCTTTTGCAGTGACCGTGA
EST: gi|71772130|gb|DR970067.1|DR970067
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATAT
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATAT
EST: gi|148969662|gb|EE020526.2|EE020526
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|71433771|gb|DR814821.1|DR814821
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAA-G                         TTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGG
EST: gi|211089789|gb|FL379367.1|FL379367
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccctgtgtatgttcatgttaaactctcaattccaacatgttgtttgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACTAAG
                                           tttgttttcc  CT-rich tract
               atgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtccagcttctgttgttccctgtgtatgttcatgttaaactctcaattccaacatgttgtttgttttccagTTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA