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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttagccaaaaatatttaaatggaaatgaggtgatactcaaaatgtttagtatttcaaatccttgcattttaatttaaattgatttacttatatgcagACTCAGCTGCGCATGGAGGCATTTTATTCATTCAATGAGAGATTTGCAAAAATTCGCAGCAAAAGGATTAAGAAAGCCATCAAGGGCATTACAGGCAAAA

Basic information

species Zea mays
transcript GRMZM2G388915_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G388915_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g10780.1 (Oryza sativa), 3'ss of exon 12
--catttagccaaaaatatttaaatggaaatgaggtgatactcaaaatgtttagtatttcaaatccttgcattttaatttaaattgatttacttatatgcagACTCAGCTGCGCATGGAGGCATTTTATTCATTCAATGAGAGATTTGCAAAAATTCGCAGCAAAAGGATTAAGAAAGCCATCAAGGGCATTACAGGCAAAA
  |||||| | || | |  || ||  | ||||     | |  |||| | |  |  |||     |  ||  ||||||   |    ||  | ||  | ||||||||||| || ||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||
ttcatttaactaagagtgatttaaccggaatgtcagca-atccaaagtctgcaaaattg-ggttatttaaattttacagtttcatgtgtcacacacatgcagACTCAACTACGCATGGAGGCGTTTTACTCATTCAATGAGAGATTTGCAAAAATTCGTAGCAAAAGGATTAAGAAAGCTATCAAGGGTATTACAGGGAAAA

upper sequence: GRMZM2G388915_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA01G16370.1 (Glycine max), 3'ss of exon 17
----------------------------------------------------------cattta--gccaaaaatatt-taaatggaaatgagg--tgatactca--aaatgtttagtattt---caaatccttgcattttaa-----tttaaattgatttacttat---atgcagACTCAGCTGCGCATGGAGGCATTTTATTCATTCAATGAGAGATTTGCAAAAATTCGCAGCAAAAGGATTAAGAAAGCCATCAAGGGCATTACAGGCAAAA
                                                           ||| |  |   ||| || | | |     ||| | |  |  || |     | ||| |||| | |   ||| || |   ||| | |      | | |    |||| |  |   ||| |||||||  ||||  |||| ||||||||    || ||||| ||||||||||||||||| || ||||| |||||||||||  | || || || || || ||  
gttattttgttttattgatctgctccccctttttactgactgttttatatttttattgtattaaaagttgaaattaatatgatcactaatcaagctttctaattgttgattgtctagtgtcttctcaattcttattattatgaatatcctgataccagtttaatcttttaatgtagACTCAATTGCGGTTGGAAGCATTTTACAATTTTAATGAAAGATTTGCAAAAATTCGTAGTAAAAGAATTAAGAAAGCGGTAAAAGGAATCACTGGTAAGC
















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|166533313|gb|EG066459.1|EG066459
EST:     CTGCTTCCAGTTTTGAGAGAGTATAATAAACACGAG                         ACTCAGCTGCGCATGGAGGCATTTTATTCATTCAATGAGAGATTTGCAAAA
genomic: CTGCTTCCAGTTTTGAGAGAGTATAATAAACACGAGgttcgtctag ... ttatatgcagACTCAGCTGCGCATGGAGGCATTTTATTCATTCAATGAGAGATTTGCAAAA
EST: gi|166495014|gb|EG050009.1|EG050009
EST:     AAGCTGATGAACTGCTGCTTCCAGTTTTGAGAGAGTATAATAAACACGAG                         ACTCAGCTGCGCATGGAGGCATTTTA
genomic: AAGCTGATGAACTGCTGCTTCCAGTTTTGAGAGAGTATAATAAACACGAGgttcgtctag ... ttatatgcagACTCAGCTGCGCATGGAGGCATTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttagtatttcaaatccttgcattttaatttaaattgatttacttatatgcagACTCAGCTGCGCATGGAGGCATTTTATTCATTCAATGAGAGATTTGCAAAAATTCGCAGCAAAAGGATTAAGAAAGCCATCAAGGGCATTACAGGCAAAA
                                        tttactt  CT-rich tract
                   ttgcattttaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttagccaaaaatatttaaatggaaatgaggtgatactcaaaatgtttagtatttcaaatccttgcattttaatttaaattgatttacttatatgcagACTCAGCTGCGCATGGAGGCATTTTATTCATTCAATGAGAGATTTGCAAAAATTCGCAGCAAAAGGATTAAGAAAGCCATCAAGGGCATTACAGGCAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - -aaaaata
- - - - - - - - - - - - - - - - - - -actcaaa