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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acataagtgctgtactgcgccgcagaggcccccttgcgaccggacaattacatgtggacctgcatgcatttatggactaacggatgcatttaccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTCTATAGACCACTCATCCGGTCCGGGCTGGCCTTTGGGGCCAGGCGGTGGC

Basic information

species Zea mays
transcript GRMZM2G026643_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026643_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g45250.1 (Oryza sativa), 3'ss of exon 6
acataagtgctgtactgcgccgcagaggcccc--cttgcg-accggac----aattacatgtggacctgcatgcatttatggactaacggatgcatttaccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTCTATAGACCACTCATCCGGTCCGGGCTGGCCTTTGGGGCCAGGCGGTGGC
       || |||| ||| | ||||||  | |  ||   | |  | ||    |   |||||       || ||||||||||| ||||||||||||||||||||||||||||||||||| ||| ||||||||||||| ||||| ||||| |||||||||||  | |||||| | ||||| || || |||||||| |||||||| ||||
-------tgttgtattgcactgcagagctctcatctgatgtattgcacctaaagacacatgcatgtgggcgtgcatttatgggctaacggatgcatttaccctgtagGTCACATGGGTTGAGCATACGGAATACGATGAGGCATCAGTGCACCAGCTCTACCGTCCACTCCTTCGGTCTGGTCTCGCCTTTGGCGCCAGGCGTTGGC
















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|211022955|gb|FL081004.1|FL081004
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211022960|gb|FL081009.1|FL081009
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211456527|gb|FL289846.1|FL289846
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211022956|gb|FL081005.1|FL081005
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211022959|gb|FL081008.1|FL081008
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211022962|gb|FL081011.1|FL081011
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211022953|gb|FL081002.1|FL081002
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211022958|gb|FL081007.1|FL081007
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGNACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|76929403|gb|DV172000.1|DV172000
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211456521|gb|FL289840.1|FL289840
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211022951|gb|FL081000.1|FL081000
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211418991|gb|FL080999.1|FL080999
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|74245648|gb|DT653562.1|DT653562
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|71437534|gb|DR818584.1|DR818584
EST:     GCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211022963|gb|FL081012.1|FL081012
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|211456524|gb|FL289843.1|FL289843
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAAGGCGTCAGTACACCAGCT
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGA-GGCGTCAGTACACCAGCT
EST: gi|211022957|gb|FL081006.1|FL081006
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|149072468|gb|EE160744.2|EE160744
EST:     GGTTGCCTTCTGGCTGTGTGATGCANGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
EST: gi|50333151|gb|CO528277.1|CO528277
EST:     GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAG                         GTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC
genomic: GGTTGCCTTCTGGCTGTGTGATGCAGGACACTCCCAATGGCTACTGCAAGgtactagcaa ... taccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacatgtggacctgcatgcatttatggactaacggatgcatttaccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTCTATAGACCACTCATCCGGTCCGGGCTGGCCTTTGGGGCCAGGCGGTGGC
                             gactaac  putative branch site (score: 1)
                                           tttaccct  putative PPT
                      atttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acataagtgctgtactgcgccgcagaggcccccttgcgaccggacaattacatgtggacctgcatgcatttatggactaacggatgcatttaccctgtagGTCACATGGGTAGAGTATACGGAATACGACGAGGCGTCAGTACACCAGCTCTATAGACCACTCATCCGGTCCGGGCTGGCCTTTGGGGCCAGGCGGTGGC

- - - gtgctgt
- - - - - - - - - gccgcag
- - - - - - - - - - - - - - - - - - - - - - - - - catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatgca