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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgttttatttctttcctctcttgcatatgttttatttctttcctcccttgcatagttctaaaggtttgaatttccttgtctgtattaatgttccaatggctctag

Basic information

species Zea mays
transcript GRMZM2G131324_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 6
GTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgttttatttctttcctctcttgcatatgttttatttctttcctcccttgcatagttctaaaggtttgaatttccttgtctgtattaatgttccaatggctctag
|||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||| ||||||||||||| ||||| || |||      || | ||| |    |   |   | ||| | ||  |||    ||||  || || |                           
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgttt-atttcatttctc------atttatttaaagattcaaccatcctgctttgtattaatatcttgatgtttctag---------------------------

upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 6
GTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgttttatttctttcctctcttgcatatgttttatttctttcctcccttgcatagttctaaaggtttgaatttccttgtctgtattaatgttccaatggctctag
|||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||| |||||| |||||||||| ||||| ||||||||||||| ||||| || |||  ||   ||    ||    |  |||| | ||| ||   |||   | |     ||| || |                           
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCGCCAACAAAAAGGATGTGGAAGAgtatgttt-atttcatttctcctttatttaaagatt-caaccatcctgctttgtattaatctcttgat----gttttctag---------------------------

upper sequence: GRMZM2G131324_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S234_26V6.2 (Physcomitrella patens), 5'ss of exon 7
GTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgttttatttctttcctctcttgcatatgttttatttctttcctcccttgcatagttctaaaggtttgaatttccttgtctgtattaatgttccaatggctctag--
| || |||||||| || ||||||||||||||||| ||||||||||| |||||  | ||  | ||| | |||||  || |||||||    ||  | ||   |||    || | | ||    | ||||  | ||  |  | |      |  || |  || || || ||       || |  ||| ||  || | |  |||    |   |   
GCTGTATGGCTTCGCTGTCTGCTATGATTCAGCTAGAACTTCCTCACATCAATGTGCTGACGAAGGTTGATCTTCTCCCCAACAAGCGCGACATTGATAGgta-aagttgtgttttcaaacgcttgt-tgtgcctagtgt------tgactagttta-ttttacagtaacctcttccaatgtgtgggttga-gcaccatcaacagaatcg

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|22818869|gb|BU498959.1|BU498959
EST:     AGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACATGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|76293904|gb|DV033472.1|DV033472
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|76281817|gb|DV021385.1|DV021385
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAAC-AAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|67031739|gb|CO460488.1|CO460488
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTTCTT-CACAGCTGAATCGGCAGA
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTT-CTTTCACAGCTGAATCGGCAGA
EST: gi|32807837|gb|CD960071.1|CD960071
EST:     GATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: GATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|32792814|gb|CD945050.1|CD945050
EST:     GATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: GATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|76016034|gb|DT943204.1|DT943204
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|71758032|gb|DR955969.1|DR955969
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|76010883|gb|DT938053.1|DT938053
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|148995051|gb|EE034364.2|EE034364
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTTTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|24764738|gb|CA399901.1|CA399901
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCACCAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|78113480|gb|DV531871.1|DV531871
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|71758174|gb|DR956111.1|DR956111
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTCTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|111197436|gb|EE295571.1|EE295571
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCGGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|211012560|gb|FL439511.1|FL439511
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|87156287|gb|DY401076.1|DY401076
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACATGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
EST: gi|60343210|gb|DN210183.1|DN210183
EST:     AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGA                         GTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT
genomic: AACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgtttta ... atggctctagGTACCTGGACCCGAATGCACAGGTTCTTCTTTCACAGCTGAATCGGCAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCATGGCTTCTCTATCTGCTATGATTCAGCTTGAACTTCCTCATATCAACATCCTTTCAAAGATGGATCTGGTCTCCAACAAAAAAGATGTAGAAGAgtatgttttatttctttcctctcttgcatatgttttatttctttcctcccttgcatagttctaaaggtttgaatttccttgtctgtattaatgttccaatggctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG