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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_T03
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|211360698|gb|FL393782.1|FL393782
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGNTAGCACATCCTTGGCTGGTGCAACACTAGGNTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|31355374|gb|CD439731.1|CD439731
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|149082633|gb|EE171834.2|EE171834
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|149083192|gb|EE172463.2|EE172463
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|31355588|gb|CD439945.1|CD439945
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|148996907|gb|EE035711.2|EE035711
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211063244|gb|FL401231.1|FL401231
EST:     ATCTCGCCAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211266596|gb|FL404017.1|FL404017
EST:     ATCTCGCGAAGGATCTTGTGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGCTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|31354767|gb|CD439124.1|CD439124
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|78078828|gb|DV507240.1|DV507240
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|148981335|gb|EE027589.2|EE027589
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|148977355|gb|EE026050.2|EE026050
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211349168|gb|FL426325.1|FL426325
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         G-TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|148971787|gb|EE022525.2|EE022525
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|148953947|gb|EC899333.2|EC899333
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|31355150|gb|CD439507.1|CD439507
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|78075828|gb|DV504262.1|DV504262
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211465272|gb|FL339432.1|FL339432
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211210064|gb|FL412311.1|FL412311
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGG
EST: gi|149055222|gb|EE156147.2|EE156147
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         --TGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGGTGCAACACTAGGTTCTTTTACTG
EST: gi|211157837|gb|FL370475.1|FL370475
EST:     ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGG---G                         G-TGGGTGGTTAGCACATCCTTGGCTGG
genomic: ATCTCGCGAAGGATCTTGGGATTGCTGAAAATGCTGTCTTGCAGGGTATGgcatactttt ... tgttactcagGGTGGGTGGTTAGCACATCCTTGGCTGG


 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