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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccacttgcctcttaaatttcctgtctgatgcgattcaacgtcctgtggagggttcctgttctttcttccgatgtcacttggactgaatataaccttttatgcag

Basic information

species Zea mays
transcript GRMZM2G060564_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060564_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 5'ss of exon 5
GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccacttgcctcttaaatttcctgtctgatgcgattcaacgtcctgtggagg-gttcctgttctttcttccgatgtcacttggactgaatataaccttttatgcag
||||| || |||||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||| | || || |||||||||||||||    ||||  ||||||   ||   ||| | |     ||  | ||    |      |||||  |||| |    | ||  ||||      ||  |   | |||  || ||
GTGTTTCTGTGCTTTGGTAATTCAGTTGCTTCAACCCGCTTCTTGCTCCAAGATGAATTCAACATACAGACAACTAAATGCGATAACTGCATCATTgtactgtcactgtcctcttg--ttgtttgttttactaacttttaggtataattcctatgttccctttctatgagactataacactgcagaagatcact-cttttcctgtag

upper sequence: GRMZM2G060564_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G37590.1 (Glycine max), 5'ss of exon 5
GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccacttgcctcttaaatttcctgtctgatgcgattcaacgtcctgtg-gagggttcctgttctttcttcc----gatgtcacttggactgaatataac-cttttatgcag
|| ||||| |||||||| |||||||| || |||||||||||  |  ||||||||||||||||||| || ||||| || ||||| || ||||| ||||||    | ||  |  | |  || | || |    |   ||||| || |   |  |   |    |||| | | |||     ||| |    |  | |  || |||| ||||| |  ||
GTTTTCCTCTGCTTTGGAAATTCAGTCGCCTCAACCCGCTTTCTATTGCAAGATGAATTTAACATTCAAACCACGCAATGTGATAATTGCATTATTgtact--ctctccctccctctatctgctttacacttgcattcaccgccagatacgcatgcaaatgttttattttctcattgatattctgttaattacatgtaactcttttgtttag

upper sequence: GRMZM2G060564_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G01990.3 (Glycine max), 5'ss of exon 4
GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccacttgcct--cttaaatttcctgtctgatgcgattcaacgtcc--------tgtggagggttcctgttctttcttcc----gatgtcacttggactgaatataac-cttttatgcag
|| ||||| |||||||| |||||||| || ||||| |||||  |  ||||||||||||||||||| || || || || ||||| || ||||| ||||||    | ||  ||   | |  || | || |    |   ||||| |  |         ||   | | ||  | || ||| ||||    ||| |    |  | |  || |||  ||||| |  ||
GTTTTCCTCTGCTTTGGAAATTCAGTCGCCTCAACTCGCTTTCTATTGCAAGATGAATTTAACATTCAAACTACGCAATGTGATAATTGCATTATTgtactctctctctccctccctctatctgctttacacttgcattcaccaccagatacatatgcaaatgctttttttttttttttccaaatgatattctgttaattacatgtaattcttttgtttag

upper sequence: GRMZM2G060564_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0025g00130.t01 (Vitis vinifera), 5'ss of exon 5
GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccacttgcctcttaaatttcctgtctgatgcgattcaacgtcctgtggagggttcctgttctttcttcc-gatgtcacttggactgaatataaccttttatgcag
||  |||| |||||||| ||||| || ||||||||||||||  || |||||||||| || ||||||||||| ||  | |||||||| ||||||||||||    |   ||| |  | |||          |  | | || |    |  | |    |   |  ||||  | || | ||  |  | |                       
GTTCTCCTCTGCTTTGGAAATTCGGTAGCATCAACCCGCTTTCTGTTGCAAGATGAGTTCAACATACAGACAACAAAATGTGACAATTGCATCATTgta----cgtatgctttctcaatgaatcaatcaaaaccaatctatacacatttgcatttggttaatcttgttacctgctgatatgtag-----------------------

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|211520836|gb|FL034043.1|FL034043
EST:     TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATT                         GGCTTCATGTTATGCCTTCAA
genomic: TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccac ... ttttatgcagGGCTTCATGTTATGCCTTCAA
EST: gi|211397637|gb|FL034037.1|FL034037
EST:     TGCAAGATGAATTTWACATACAGACCACTCAGTGTGACAACTGCATCATT                         GGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCA
genomic: TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccac ... ttttatgcagGGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCA
EST: gi|148930645|gb|EC872835.2|EC872835
EST:     TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATT                         GGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCA
genomic: TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccac ... ttttatgcagGGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCA
EST: gi|211520833|gb|FL034040.1|FL034040
EST:     TGCAAGATGAATTTAACATACAGACCACTCAGTGCGACAACTGCATCATT                         GGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCA
genomic: TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccac ... ttttatgcagGGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCA
EST: gi|211397638|gb|FL034038.1|FL034038
EST:     TGCAAGATGAATTTNACATMCAGACCACTCAGTGTGACAACTGCATCATT                         GGCTTCATGTTATGCCTTC
genomic: TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccac ... ttttatgcagGGCTTCATGTTATGCCTTC
EST: gi|211520835|gb|FL034042.1|FL034042
EST:     TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATT                         GGCTTCATGTTATG
genomic: TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccac ... ttttatgcagGGCTTCATGTTATG
EST: gi|76011810|gb|DT938980.1|DT938980
EST:     TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATT                         GGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCA
genomic: TGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccac ... ttttatgcagGGCTTCATGTTATGCCTTCAACAAGTTGCTTGCATCTTCTCTATAGTTGCA
EST: gi|211520839|gb|FL034046.1|FL034046
EST:     GCAAGATGAATTTRACATACAGACCACTCAGTGCGACAACTGGCATCATT                         GGCTTCATGTTATGCCTTCAACAAGTTGCTT
genomic: GCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTG-CATCATTgtaacaccac ... ttttatgcagGGCTTCATGTTATGCCTTCAACAAGTTGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTCCTTTGCTTTGGCAATTCAGTTGCATCAACCCGCTTCTTGCTGCAAGATGAATTTAACATACAGACCACTCAGTGTGACAACTGCATCATTgtaacaccacttgcctcttaaatttcctgtctgatgcgattcaacgtcctgtggagggttcctgttctttcttccgatgtcacttggactgaatataaccttttatgcag

- - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGATG