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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatttgtttgcttttttatcttggtagtattccttacttcaaataatgtgtgtttgactgacatgatggtaaaaaacaaatacag

Basic information

species Zea mays
transcript GRMZM2G035595_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035595_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g16600.1 (Oryza sativa), 5'ss of exon 5
GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatttgttt--gcttttttatc-----ttggtagta----ttccttacttcaaataatgtgtgtttgactgacatgatggtaaaaaacaaatacag-------------------
||||||||| ||||||||||| ||| | ||||| ||||| ||||||||||| |||||||||||||| ||||||||||| ||||||  | |||||| ||     |||  |  |    | ||| |||||| |  |  |||||| || |  |||||||  | |   | | |   |                   
GTATGCATATGCTGTTGCTAGTGCACTCCATGGGGTTCAACATATCCTTCGAAAAGATTTCATGATTCAGgtgctctacttgtttatgtttttttgtcaatgcttgacaacagacttgcctgacttcagagtagttgtgtt-gagtttcatgatg--agagtgctattgatggtccagtaaaaatttgcag

upper sequence: GRMZM2G035595_T04 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0009g03360.t01 (Vitis vinifera), 5'ss of exon 5
GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatttgtt-tgcttttttatcttggtagtattccttacttcaaataatgtgtgtttgactgacatgatggtaaaaaacaaatacag-------------
||||||||| ||||| ||    ||||||||||| || || ||||||||||||||||| |||||| | |||||  |  || |||  || |   | |   ||    |   | || ||||   |||||| | |  || |  ||    | | |  ||||   |                
GTATGCATATGCTGTAGCATCTGCATTGCATGGTGTGCAGCATATCCTTCGTAAAGACTTCATGCTACAGgt-ttgcatgtgtcctgatgactcaatctgcatatcaccatttcttct--taatgtttata-gaatatcacatggatcactaacatgcatcttgtaagttttcag
















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|5928606|gb|AW056003.1|AW056003
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGA-TTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|211142481|gb|FL118078.1|FL118078
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|71441274|gb|DR822324.1|DR822324
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|148949122|gb|EC894553.2|EC894553
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|211025730|gb|FL435838.1|FL435838
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|211541587|gb|FL476015.1|FL476015
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|71759438|gb|DR957375.1|DR957375
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|211246948|gb|FL479530.1|FL479530
EST:     GGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|86472181|gb|DY238551.1|DY238551
EST:     CGCATTGCATGGAGTTCATCAT-TCCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: CGCATTGCATGGAGTTCATCATAT-CCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|149009585|gb|EE154018.2|EE154018
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|5928615|gb|AW056012.1|AW056012
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGA-TTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|5816276|gb|AI987192.1|AI987192
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGA-TTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|84970100|gb|DV171467.2|DV171467
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
EST: gi|4776320|gb|AI665323.1|AI665323
EST:     GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAG                         CCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT
genomic: GCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatt ... acaaatacagCCACCTTTTGATACAAAGCTCCAGAATACATTTATAATCCACTTCACTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGCATACGCTGTTGCTAGCGCATTGCATGGAGTTCATCATATCCTTCGTAAAGATTTCATGATCCAGgtgctctatttgtttgcttttttatcttggtagtattccttacttcaaataatgtgtgtttgactgacatgatggtaaaaaacaaatacag

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