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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCAATCATGGCCGTCGGGGCATCAGAACCCACCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttcttgtgcctggcggaacatgtcctttcgtgccaactattttttgtttgatggttttctttttgcttgattttacacttccgctcacctgatcaatgcatgtag

Basic information

species Zea mays
transcript GRMZM2G165176_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165176_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 5'ss of exon 5
GGAGCAATCATGGCCGTCGGGGCATCAGAACCCACCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttc-ttgtgcctggcggaacatgtcctttcgtgccaactattttttgtttgatggttttctttttgcttgattttacacttccgctcacctgatcaatgcatgtag-
|| |||||||||||||| ||  ||||| |||| ||  |||||||||||||||||||||| |||||||||||||| ||||||||||||| |||  |  |  |||  |  |||  | |||||   | | | | || |         ||||| |||| |||| ||||          ||||||||| |||| ||| |   
GGTGCAATCATGGCCGTTGGATCATCACAACCAACACTTGTTGGTACAAAAGATGGTAGTATTGGGATCAAGAACCAAATGCAGgtaaatttaatcatagctg-tgccacactttctttctcacaagccaattatga------agtttttttttggcttaattt----------ctcacctgaccaatacatcttag

upper sequence: GRMZM2G165176_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 5'ss of exon 5
GGAGCAATCATGGCCGTCGGGGCATCAGAACCCACCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttcttgtgcctggcggaacatgtcctttcgtgccaactattttttgtttgatggttttctttttgcttgattttacacttccgctcacctgat-caatgcatgtag
|||||||||||||| || || ||||||||||| ||| ||||||  || || |||||| | ||||| || ||||  || |||||||||| |||| |  |         |  | ||    |      |  |||| |      |||  |||   |||  || |   |   ||| ||||      || ||||   || ||
GGAGCAATCATGGCGGTTGGAGCATCAGAACCAACCGTTGTTGCCACCAAGGATGGTCGGATTGGCATGAAGAGCCAGATGCAGgtaattttccttag---------atctctctccccaaattgagaatttct-acaccatgtgtttggatttattttacagt-ttcttacgctgggaacatgcaatatctgcag
















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|71422995|gb|DR805914.1|DR805914
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|32933663|gb|CF038475.1|CF038475
EST:     TACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: TACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|31349635|gb|CD433992.1|CD433992
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|50333015|gb|CO528141.1|CO528141
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|148963616|gb|EE014658.2|EE014658
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|4775958|gb|AI664961.1|AI664961
EST:     AAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: AAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|149089772|gb|EE179047.2|EE179047
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|101400418|gb|EB822024.1|EB822024
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|5018378|gb|AI714571.1|AI714571
EST:     AAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: AAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|71430961|gb|DR812011.1|DR812011
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTCCCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|37398364|gb|CF636494.1|CF636494
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|31356951|gb|CD441308.1|CD441308
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|83278298|gb|DV942306.1|DV942306
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|211076029|gb|FL472760.1|FL472760
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
EST: gi|149108559|gb|EE189711.2|EE189711
EST:     CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAG                         GTAAATGTTCCCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT
genomic: CCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttct ... atgcatgtagGTAAATGTTACCGCCGATCATCGGGTTATTTATGGAGCTGACCTTGCTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCAATCATGGCCGTCGGGGCATCAGAACCCACCATTGTTGGTACAAAAGATGGTAGAATTGGGATCAAGAATCAAATGCAGgtaagtttcttgtgcctggcggaacatgtcctttcgtgccaactattttttgtttgatggttttctttttgcttgattttacacttccgctcacctgatcaatgcatgtag

- - - - - - - - - - - - - - - - - - - - - - - -  AAGATG