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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatctctccttttggttgcaagttggttcatctgatccttattttcgttggcgggcttggggttctactactaccaaggatagtctttactgtgagttagatgacctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC

Basic information

species Zea mays
transcript GRMZM2G006130_T06
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 14
----------------gtgatctctccttttgg----ttgcaagttggttcatctgatccttattttcgttggcgggct-tggggttctactact--accaaggatagtctttactgtgagttag-atgacctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC
                   |||| | ||||  |    |||  |       ||| ||| | ||  | | | | | |   | |   | |||||||    |   |  |   | || | ||| | ||    |    | ||||||||||| | ||||||||||||||||| || ||||||||||||||| ||||||| |||||
gtgatctttccttgaaacaatcttttctttctgggtcttgtgacagatcacatttgagctttcctctgggtagggctttattaagatctactaacaaatgcaacaagatattcattgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTCTTCGTGAACAACAATGATCAAAC

upper sequence: GRMZM2G006130_T03 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os12g03470.2 (Oryza sativa), 3'ss of exon 14
----------------gtgatctctcctttt--ggttgcaagttggttca--tctgatccttattttcgttggcgggcttggggttctactactaccaaggatag--tctttactgtgagttag-atgacctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC
                   |||| | ||||   ||| |   |   | |||  | ||| | ||   | ||| ||      |   | |||||||  |      ||    | |||||||| | ||    |    | ||||||||||| | ||||||||||||||||| || ||||| ||||||||| ||||||| |||||
gttatctttccttgaaacaatcttttctttccgggtcgtgtgacagatcacatttgagcttt-cctgcgtagggctttattaagatctactaacaaatgcaatgagatatttactgtaacttcttgttggttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGATCAAAC

upper sequence: GRMZM2G006130_T03 (Zea mays), 3'ss of exon 14
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 14
gtgatctctccttttggttgcaagttggttcatctgatccttattttcgttggcgggcttggggttctactactaccaaggatagtctttactgtgagttagatgacctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC-
                          | | | | |||     ||||   ||  | ||||| |   || ||||     ||  ||    |    |     |   ||||| |||||||||||| || ||| | ||||||||||| ||||||||||| ||||||   |||||  | || 
--------------------------gttccctttga-----atttctcttcccaggctttgatctcaacta----aaaacatcaaataagttaaacatcttatgac-tttttgcagTGACATTGTTGAAATGGCAAGTTATGCTCCACTCTTTGTGAACACAAATGAT-AGACG

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|211378660|gb|FL357038.1|FL357038
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
EST: gi|211495379|gb|FL350690.1|FL350690
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
EST: gi|211474807|gb|FL320108.1|FL320108
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
EST: gi|32843955|gb|CD983636.1|CD983636
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATTGTTCAGATGGCAAGTTACGCACCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
EST: gi|18654846|gb|BM499651.1|BM499651
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
EST: gi|211258110|gb|FL346334.1|FL346334
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
EST: gi|150037294|gb|DY843524.1|DY843524
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAG                         TGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA
genomic: CTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctc ... ctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttctactactaccaaggatagtctttactgtgagttagatgacctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC
                                            cctttttgc  CT-rich tract
                                              ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatctctccttttggttgcaagttggttcatctgatccttattttcgttggcgggcttggggttctactactaccaaggatagtctttactgtgagttagatgacctttttgcagTGATATCGTTCAGATGGCAAGTTACGCTCCACTCTTCGTGAACGACAATGACCAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG