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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttcttccaccttcccctacactatgtttccaagctactcgattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAG

Basic information

species Zea mays
transcript GRMZM2G008647_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g06430.2 (Oryza sativa), 3'ss of exon 9
gtactttcttccaccttcccctacactatgtttccaagctactcgattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAG
                             ||    ||  | |     || ||| | ||| || |||||||||   || ||| ||||   |   | |  |||| ||||||||   ||| |||| | ||||| || |||||||   ||||||||||||||||||| ||||||||||| ||||||||||||||  ||||||||||||| |||||| ||||||||
-----------------------------gtactaaattttcatctctgtttttaaatt-ttgttatgtaggtt-tggcatcgtcactgtgtgaat-ttaaccattttgct---aaagcagGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAGAAG

upper sequence: GRMZM2G008647_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 9
gtactttcttccaccttcccctacactatgtttccaagctactcgattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAG
                             ||    ||  | |     || ||| | ||| || |||||||||   || ||| ||||   |   | |  |||| ||||||||   ||| |||| | ||||| || |||||||   ||||||||||||||||||| ||||||||||| ||||||||||||||  ||||||||||||| |||||| |||||   
-----------------------------gtactaaattttcatctctgtttttaaatt-ttgttatgtaggtt-tggcatcgtcactgtgtgaat-ttaaccattttgct---aaagCAGGTACGGAAAGATCTATGTGAACTCTGCAAAGAAGATCATGGAGAAGGGCTCTGAATACACTAAGAAGGAATCTGAGAGGCTTCAACGCATGTTGGAG---
















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|26558990|gb|CA831225.1|CA831225
EST:     CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAA                         GCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
genomic: CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtactttctt ... tctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
EST: gi|87156320|gb|DY401109.1|DY401109
EST:     CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAA                         GCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
genomic: CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtactttctt ... tctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
EST: gi|26559048|gb|CA831283.1|CA831283
EST:     CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAA                         GCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
genomic: CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtactttctt ... tctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
EST: gi|22520845|gb|BU079656.1|BU079656
EST:     CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAA                         GCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
genomic: CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtactttctt ... tctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
EST: gi|22520856|gb|BU079667.1|BU079667
EST:     CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAA                         GCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
genomic: CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtactttctt ... tctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
EST: gi|87156605|gb|DY401394.1|DY401394
EST:     CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAA                         GCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC
genomic: CTCTCTAAAATAGAAGAGGATGTTGCTAAGCTCAGCGGTTCTGCAGCCAAgtactttctt ... tctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAG
                                      ttttgcttct  CT-rich tract
                                taactatttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttcttccaccttcccctacactatgtttccaagctactcgattgatttaacattcttattatgtaggcagtgccattgtcaaattacaagtactaactattttgcttctaaaccagGCATGGAAATATATATGTGACAGCTGCAAAGAAGATCATGGACAAGGGCTCTGACTACACTAAGAAGGAGACTGAGAGGCTTCACCGCATGCTGGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA