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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgctatttccatgacacctgctctatgtactttcagaggactagaatcatggggtacctgcaaaattgattgtgatcccgacatctaaatgaaaagaaattcaaggtttaatgaatcttctactattatttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG

Basic information

species Zea mays
transcript GRMZM2G004352_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g54640.1 (Oryza sativa), 3'ss of exon 4
gtattgctatttccatgacacctgctctatgtact--ttcagaggactagaatca--------tggggtacctgcaaaat-----tg-attgtgatcccg--acatctaaatg-aaaagaaattcaaggt----ttaatgaatcttctactat-tatttctgcc--agGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG
       ||||||| ||  |||| |||| ||| ||  |   ||    || ||  |        |    | | | ||| ||     || |||  | | | |  |||  |   || |||| || ||    ||    ||||| ||  | |||  || ||| |||  |  ||||||||||||| || || || ||||||||||||||||| |||||||| ||||||||| |||||||  |  |||| ||
------gtatttccttgctacctcctctttgtgctactctggattgataaaaataatccttttttttttccttacaagatataagtgcattaggcttcggtcacaggttcctgcaaaataattttctagtgatattaataaacatcctatgatatatctctatctcagGATTGGGGCTTTTTCGTTCCTTACTTGATTGGAAGCATCTCATTGATAGTATTGGCTATCGGAAGTATTTCTCCCGG

upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA05G31720.1 (Glycine max), 3'ss of exon 4
gtattgctatttccatgacacctgctctatgtactttcagaggactagaatcatggggtacctgcaaaattgattgtgatcccgacatctaaatgaaaagaaattcaaggtttaatgaatcttctactattatttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG
                      |  ||||  ||||| |     |||  || || ||   ||||  |||        | ||   ||||| |   |          || |  | | ||  || |     |  |   |||   ||||||||||||||||||| || ||||||||||| || || |||||  | || |||||||| || ||| |  | |||||
------------------tttttcttctaactacttcccacacactc-aacca-ggcagaccttaaaa--------taattttgacattttttt----------tccatctctgattgatgtg----tgctgactcttgtagGATTGGGGCTTCTTTGTACCGTACTTGATTGGGAGTATCTCATTAGTGGTTTTGGCTGTGGGTAGCATATCCCCAGG

upper sequence: GRMZM2G004352_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G14970.1 (Glycine max), 3'ss of exon 4
gtattgctatttccatgacacctgctctatgtactttcagaggactagaatcatggggtacctgcaaaattgattgtgatcccgacatctaaatgaaaagaaattcaaggtttaatgaatcttctactattatttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG
                 |    |  ||||  ||||| |     |||     ||    | |      ||| | ||| |||        || |  |   |      |  | || |  |||||||| ||               |||||||||||||||||| || ||||||||||| || ||||||||  | || |||||||| || ||| |  | |||||
-----------------atttttcttctaactacttcccacacact----ccaccaagcagaccttaaaataattttgacttttttttccatctctga------ttgatgtgtgctgaatcttgta---------------gGATTGGGGCTTCTTTGTACCATACTTGATTGGGAGTATTTCATTAGTGGTTTTGGCTGTAGGTAGCATATCCCCAGG

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|50329898|gb|CO525024.1|CO525024
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|211212631|gb|FL412327.1|FL412327
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTTCATTG
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTT-CATTG
EST: gi|148954649|gb|EC900096.2|EC900096
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|149084909|gb|EE174419.2|EE174419
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|211463633|gb|FL380567.1|FL380567
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTT
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTT
EST: gi|211057978|gb|FL426568.1|FL426568
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTG-AAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|76010526|gb|DT937696.1|DT937696
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCAGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|71313543|gb|DR793346.1|DR793346
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|211110152|gb|FL388603.1|FL388603
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|37417290|gb|CF646298.1|CF646298
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|149100298|gb|EE186363.2|EE186363
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|211472091|gb|FL427745.1|FL427745
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGG
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGG
EST: gi|148930743|gb|EC873038.2|EC873038
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
EST: gi|71317339|gb|DR795363.1|DR795363
EST:     TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGG                         GATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA
genomic: TTGTGGGTACCACTGGATTCTTAGCCGTCCTTGCAGGCCAGCTCCCTGGGgtattgctat ... tttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaaatgaaaagaaattcaaggtttaatgaatcttctactattatttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG
                                          ttatttct  CT-rich tract
                                  ttctactattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgctatttccatgacacctgctctatgtactttcagaggactagaatcatggggtacctgcaaaattgattgtgatcccgacatctaaatgaaaagaaattcaaggtttaatgaatcttctactattatttctgccagGATTGGGGCTTCTTTGTCCCCTACTTGATTGGAAGCATTTCATTGATCGTATTGGCTGTCGGAAGCGTCGCTCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG