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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttggttatgcagtgtcttgaatcttctgaactctgcctctcaaataacaaaccctacttactttctggtcatgcaagctttcatgcagcatgcc...

Basic information

species Zea mays
transcript GRMZM2G471805_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g57330.2 (Oryza sativa), 5'ss of exon 5
TACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttggttatgcagtgtcttgaatcttctgaactctgcctctcaaataacaaaccctacttactttctggtcatgcaagctttcatgcagcatgcc--------------
  ||||||||||  | || |||||||||||||||||||| |||||||| ||||| |  || ||||| |||||||| |||||||| ||||||||||| |||||||||||   | |||  || |    | |||  ||  |  |   |||||||| |  | ||||||||||     |  |||| |  ||||||||  ||||                
CTCCATCGGCTCTGTCACCGTTGCAGAATTGGACTGGGGTAACAAAGATCATATAAGAGCTGTTGATCCTCCATTCGATTACATCATTGGAACTGATGTTgtaagttt---tctgcgctggc----agctt--gagtttggtgcctcaaatagcttatcctacttact-----gatatgctaaatttcatgcgtcatgatatttcagttgttct

upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA11G19970.2 (Glycine max), 5'ss of exon 7
TACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttggttatgcagtgtct-tgaatcttctgaactctgcctctcaaataacaaaccctacttactttctggtcatgcaagctttcatgcagcatgcc-------
| |  | || || || |  || || ||  |  | |||||  |  |    ||||| ||||| ||||  ||||||||||| ||||| ||||| ||||| ||||||||| | |    |  || |||   ||   | |||| |  |  | |||   ||||        | ||| | |    |    | ||      || | | ||       
TTCATTTGGTTCGATCAAGGTGGCTGAGCTTCAGTGGGGAGATGAGAGTCATATTAAGGCAGTTGGTCCTCCATTTGACTACATCATTGGCACTGATGTTgtaagtgtagaacaggcgtttctgcaaacaatgtgaagt--gaatgtcactgaacag------ttaactctttaaaaaaaataactcattaacaacgtaccaatttaa

upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA12G08490.1 (Glycine max), 5'ss of exon 7
TACCATC-GGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttggt-tatgcagtgtcttgaatcttctgaactctgcctctcaaataacaaaccctacttactttctgg--tcatgcaagctttcatgcagcatgcc
   |||  || || || |  || || ||  |  | |||||  |  |    || || ||||| ||||  ||||||||||| ||||||||||| ||||| ||||||||| | |   | ||  |      ||   | |||| |        |  | || ||       ||| || |||   | ||  ||  ||   |     |    
-GTCATTTGGTTCGATCAAGGTGGCTGAGCTTCAGTGGGGAGATGAGAGTCACATTAAGGCTGTTGGTCCTCCATTTGACTACATTATTGGCACTGATGTTgtaagtgtagaacaggcctttctgcaaacaatgtgaagtgaatgctacttacaaaaatgtgattttaattgctgaaattatcaaaaattggttattttag---

upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv03s0017g01120.t01 (Vitis vinifera), 5'ss of exon 8
TACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttggttatgcagtgtcttgaatcttctgaactctgcctctcaaataacaa-accctacttactttctggtcatgc---aagctttcatgcagcatgcc
| |  | || ||  |    || |||||  |||||||||| ||  |||| ||||| ||||| ||| | || |||||||||| ||||||||| ||||| |||||||||||  |     ||  ||||   |      ||          ||  | || |   | ||||| |  |||  |  |     |||  |  ||  |  |    
TTCATTTGGTTCTGTCCAGGTAGCAGAGCTGGACTGGGGAAATGAAGATCATATAAAGGCAGTTAATCCACCATTTGATTTCATTATTGGCACTGATGTTgtaagtttactggatgagattctttttttgcaaaaaaaaaaaaatgcaggttaccatgacttactttcagtctcattttctgaaaagagtgaataaataa----

upper sequence: GRMZM2G471805_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv06s0061g00490.t01 (Vitis vinifera), 5'ss of exon 8
TACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttggttatgcagtgtcttgaatcttctgaactctgcctctcaaataacaaaccctacttactttctggtcatgc---aagctttcatgcagcatgcc-
| |  | || ||  |    || |||||  |||||||||| ||  |||| ||||| ||||| ||| | || |||||||||| ||||||||| ||||| |||||||||||  |     ||  ||||     || || |              || ||   | ||||| |  |||  |  |     |||  |  ||  |  ||    
TTCATTTGGTTCTGTCGAGGTAGCAGAGCTGGACTGGGGAAATGAAGATCATATAAAGGCAGTTAATCCACCATTTGATTTCATTATTGGCACTGATGTTgtaagtttactggatgagattctt----tttttgcaaaaaaaaagaaggttaccatgacttactttcagtctcattttctgaaaagagtgaataaataatttta

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|211397545|gb|FL373943.1|FL373943
EST:     ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTT                         ATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
genomic: ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttgg ... cacgttcaagATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
EST: gi|60395803|gb|DN228673.1|DN228673
EST:     ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTT                         ATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
genomic: ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttgg ... cacgttcaagATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
EST: gi|211175782|gb|FL245447.1|FL245447
EST:     ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTT                         ATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
genomic: ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttgg ... cacgttcaagATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
EST: gi|211341427|gb|FL403611.1|FL403611
EST:     ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTT                         ATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
genomic: ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttgg ... cacgttcaagATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
EST: gi|211442064|gb|FL421101.1|FL421101
EST:     ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTT                         ATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA
genomic: ATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttgg ... cacgttcaagATTTACTCAGAGCATCTGTTGCAACCTCTAATGGAGACAATTACTGCATTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCATCGGCTCAATTACAGTTGCAGAATTGGACTGGGGGAACAAAGAACATATCAAGGCCGTTGAACCTCCATTTGATTACATTATTGGAACTGACGTTgtaagtttggttatgcagtgtcttgaatcttctgaactctgcctctcaaataacaaaccctacttactttctggtcatgcaagctttcatgcagcatgcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataacaa