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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattaccatgatgtacaattgtacattggtagtattacagagatcatctgatacctctgcaatgatgtaactggtcactgttttgatctattgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG

Basic information

species Zea mays
transcript GRMZM2G040017_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 7
tattaccatgatgtacaattgtacattggtagtattacagagatcatctga-tacctctgcaatgatgta--actggtcactgttttgatctat------tgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG
     |  ||  |     || ||||||| | || ||||||   ||| |||| ||||||||||  | | ||  | || |||||| |||| ||| |      |||| | |||| |||||||||||| |||||||||| |||||||||||||||||||||||||||||||||||||| || || ||||||||||| ||||||||||||||||
-----ctctg--gccatgttatacattgtttgtcttacagg--tcacctgagtacctctgcatgggtatactattgatcactgctttgctctttgctatttgctatcagGGGGCATCTGATTCACTGAACCTACCCGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGAAACGCTGCTGAACATGCTAGTGCAATAATGTTTG

upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 6
------------------------------------------tattaccatgatgtacaattgtacattggtagtattacagagatcatctgatacctctgca--atgatgtaactggtcactgttttgatctattgctgtt----agGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG
                                          |||||   |       ||   |  | |  |  ||||   |   |  ||    | | ||||   || |  | | |  |     | |||   |  || | |     ||||||||||||| ||||||||  |  | |||||||||||   ||| || |||||||| ||||| |||||||| || |||||||| ||||| || |||||||
gtatagctatatcattttcagaatttcttgatcattaatttctattattgtacaactaaagcttctaatattcctattcttgttcttgtccataaacactgcgtcataagttcattcatagacatattgtgtttctggtctcttgcagGGAGCATCTGAGTCATTGAATATGTCAGTGGCTTTTATTTCTGTCATCTTGCTTCCAATTGTAGGCAATGCTGCAGAACATGCCAGTGCTATCATGTTTG

upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 6
tattaccatga-tgtacaattgtacattggtagtattacagagatcatctgatacctctgca--atgatgtaactggtcactgttttgatct--attgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG
  | | ||  | | |  | |  ||||||   | |||| |    || |||    |  ||||||  || |  | | |  |     || || |     |  ||   ||||||||||||| ||||||||  |  | |||||||||||   ||| || |||||||| ||||| |||||||| || |||||||| ||||| || |||||||
--tcatcaaaactctgtattcatacattcacaatattcct---attatccataaattctgcatcataagttcattcattgacattgtgtttctggtctcttgcagGGAGCATCTGAGTCATTGAATATGTCAGTGGCTTTTATTTCTGTCATCTTGCTTCCAATTGTAGGCAATGCTGCAGAACATGCCAGTGCTATCATGTTTG

upper sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 7
tattaccatgatgtacaattgtacattggta-gtattacagagatcatctgatacct--ctgcaatgatgtaactggtcactgttttgatctattgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG
  |||  ||| | | |  ||  |||||  |   | ||   ||| |     |     |   ||  |  |  | ||   ||| | ||||  |   ||  | | ||||||||||||| ||||| ||| | || ||||||||||| ||||| ||| ||||||| ||||| || ||||| ||||| ||||| |||||||| |||||||
-tttattatgctttcc--ttcaacattaatttatgttctggaggtagaaaggctattggttgtgaacagttgacaaatcaatttttttctggtttcttttcagGGAGCATCTGAGTCATTAAACATGCCAGTGGCTTTTATTAGTGTCATTCTGCTTCCAATTGTAGGAAATGCTGCTGAGCATGCCAGTGCAATTATGTTTG

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|149085153|gb|EE174657.2|EE174657
EST:     TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|211010290|gb|FL457993.1|FL457993
EST:     TTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTCTG
genomic: TTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|91868897|gb|EB400200.1|EB400200
EST:     TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|32837305|gb|CD976983.1|CD976983
EST:     TACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTCTG
genomic: TACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|60339318|gb|DN206291.1|DN206291
EST:     TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|32836604|gb|CD976282.1|CD976282
EST:     GTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTCTG
genomic: GTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
EST: gi|148972711|gb|EE023671.2|EE023671
EST:     TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAG                         GGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG
genomic: TAACACTCTGGGTGTCTTTTCTTTCTGAGTACCTAGTTAACGCCATTGAGgtattcttct ... ttgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctgatacctctgcaatgatgtaactggtcactgttttgatctattgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG
                                   ttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattaccatgatgtacaattgtacattggtagtattacagagatcatctgatacctctgcaatgatgtaactggtcactgttttgatctattgctgttagGGAGCATCTGATTCATTGAACCTACCGGTGGCTTTTATCAGTGTTATTTTGCTTCCTATTGTGGGCAATGCAGCTGAACATGCAAGTGCAATAATGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - tgatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg