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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttttctatagtagaagatagatgtctataatcactcaatgataacagttgcttctgtgcttgccatatggttcactagacatgtgtttgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTGGGGGTTCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGA

Basic information

species Zea mays
transcript GRMZM2G153704_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g04190.2 (Oryza sativa), 3'ss of exon 4
atgttttctatagtagaagatagat-gtctataatcactcaatgataacagttgct----tctgtgcttgccatatggttcactagacatgt-gtttgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTGGGGGTTCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGA
     |   | |  |  || || ||     |||   | |  ||  ||  | |   |    | |  | |||| ||||  ||||| |  ||| | ||||||  || ||| ||||||||||||||| || |||||||||| |||  ||||||||||||||| ||| |||| || || |||||||| || ||| | || |||||||||||
----gtctaagaaaaacagctaaatcaaacatagaaagttgatagtatgattctatgagatattcgtttgcaatat--ttcacaatgcattttgtttgtctcttagGATGGGTGGTTAGCACAACCCTGGCTGGTGCGACAGCAGGTTCTTTTACTGGAGGTGCTTTAGCTGACAAATTTGGACGAACACGGACGTTCATCCTGGA

upper sequence: GRMZM2G153704_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 4
atgttttctatagtagaagatagatg--tctataatcactcaatg-ataacagttgcttctgtgcttgccatatggttcactagacatgtgtttgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTGGGGGTTCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGA
|| | ||||||  |   |  ||  |   | |||  | | |   |  || ||   ||  | | |   |   | | | ||    |     |  |||  |   |||| ||||| |||||||||  | |||||||||| || || ||||| |||||||| ||| | ||||| |||||||||||  | ||||| || ||    || ||
atatattctatgttttcatttattttattttatttttattttttttatcaccaatgaatatctagct-ttacaagatttgacaatggagcattt--tgagcagGATGGGTTGTTAGCACACTCCTGGCTGGTGCCACTCTTGGTTCATTTACTGGTGGTGCATTGGCTGATAAATTTGGCAGAACAAGGACTTTTCAACTAGA
















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|78078828|gb|DV507240.1|DV507240
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211063244|gb|FL401231.1|FL401231
EST:     TGAATATCTCGCCAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211360698|gb|FL393782.1|FL393782
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGNTAGCACATCCTTGGCTGGTGCAACACTAGGNTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|148996907|gb|EE035711.2|EE035711
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|31355588|gb|CD439945.1|CD439945
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|31355374|gb|CD439731.1|CD439731
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211153701|gb|FL418638.1|FL418638
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACAT
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACAT
EST: gi|148977355|gb|EE026050.2|EE026050
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|113823106|gb|DW940246.1|DW940246
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTAC
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTA-GCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTAC
EST: gi|211157837|gb|FL370475.1|FL370475
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGGTGGGTGGTTAGCACATCCTTGGCTGG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGG-TGGGTGGTTAGCACATCCTTGGCTGG
EST: gi|148971787|gb|EE022525.2|EE022525
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|78075828|gb|DV504262.1|DV504262
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211210064|gb|FL412311.1|FL412311
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGG
EST: gi|31354767|gb|CD439124.1|CD439124
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|148981335|gb|EE027589.2|EE027589
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|149055222|gb|EE156147.2|EE156147
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211465272|gb|FL339432.1|FL339432
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|149083192|gb|EE172463.2|EE172463
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211482782|gb|FL423805.1|FL423805
EST:     AATATCTCGCGAAGGATCTTGGNNGAT-GCTGAAA-TGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGG
genomic: AATATCTCGCGAAGGATCTTGG--GATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGG
EST: gi|211349168|gb|FL426325.1|FL426325
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACT
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGG-TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACT
EST: gi|31355150|gb|CD439507.1|CD439507
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|149082633|gb|EE171834.2|EE171834
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|148953947|gb|EC899333.2|EC899333
EST:     TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211266596|gb|FL404017.1|FL404017
EST:     TGAATATCTCGCGAAGGATCTTGTGATTGCTGAAAATGCTGTCTTGCAGG                         GGTGGGTGGCTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: TGAATATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGgtatggcata ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacagttgcttctgtgcttgccatatggttcactagacatgtgtttgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTGGGGGTTCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGA
 tgataac  putative branch site (score: 2)
                                           tttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttttctatagtagaagatagatgtctataatcactcaatgataacagttgcttctgtgcttgccatatggttcactagacatgtgtttgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTGGGGGTTCTTTGGCAGATAAATTTGGGCGGACAAGAACATTCATCCTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC