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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTGTTTCTGCCTCTTCTTACTGCTGCGCTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaatttgataaatattttctaaagaggacgcagatttttctagatgttctgaatacacataattgatcatatttcttgccatggccacttgcttttgcag

Basic information

species Zea mays
transcript GRMZM2G024615_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024615_T05 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os09g13870.3 (Oryza sativa), 5'ss of exon 6
ATTGTGTTTCTGCCTCTTCTTACTGCTGCGCTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaa----aatttgataaatattttcta-aagaggacgcagatttttctagatgttctgaatacacataattgatcatatttcttgccatggccacttg--cttttgcag
|| || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||   ||| ||||||||| ||    |||   ||||  ||| | |  |||||| |  ||   | |||| | |    ||| | | | |         ||||||||     | || ||   || ||||||
ATAGTATTTCTGCCTCTTCTTACTGCTGCACTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCACTGGCAGGATGTATTTGCAGGCTCTCTGATAGgtttgcaatttcaataatataacaattatatgcaagaggtcctagcactatctaaaag----gaaaaaaaaaatccacaaccatttcttgattctggcatttctcctgttgcag

upper sequence: GRMZM2G024615_T05 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G18450.2 (Glycine max), 5'ss of exon 6
ATTGTGTTTCTGCCTCTTCTTACTGCTGCGCTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaatttgataaatattttctaaagaggacgcagatttttctagatgttctgaatacacataattgatcatatttcttgccatggccacttgcttttgcag
||||| ||  | || ||||||   || ||  |  | ||||| ||||| || ||||| || |||||||||||||||||||| ||| | || || ||||||||| |||  ||     |  || || | |            ||||| |  | ||||    |||| || |  ||   || | || ||      ||       || |||||
ATTGTTTTCTTTCCGCTTCTTGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTATTGGCATCATTGGCAAGATGTTTTTACTGGAGGGCTTATAGgtctgttgaa--gactggattttctttgt--------ttgatttattaatatgt---aaatatactt--ttctccagactttttatacgagct-----tttatgcag

upper sequence: GRMZM2G024615_T05 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G25650.1 (Glycine max), 5'ss of exon 6
ATTGTGTTTCTGCCTCTTCTTACTGCTGCGCTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaatttgataaatattttctaaagaggacgcagatttttctagatg-ttctgaatacacataattgatcatatttcttgccatggccacttgcttttgcag
 |||| ||  | ||  | ||    || ||  |  | ||||| ||||| || ||||| ||||||||||||||||||||||| ||||| || | ||||||||||||||     ||    ||      | | |  |     | ||||   || |   || |||| |        |    || | | || |||                   
CTTGTTTTCTTACCAATCCTCGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTACTGGCATCATTGGCAAGATGTGTTTGCTGGAGCTCTTATAGgtttgt-----ttcccgaag-----ccagattgattatatatttcaataaacccttttgaaaagtttctgatacgaatgtcttttaccag------------------

upper sequence: GRMZM2G024615_T05 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA10G41580.1 (Glycine max), 5'ss of exon 6
ATTGTGTTTCTGCCTCTTCTTACTGCTGCGCTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaatttgataa-atattttctaaagaggacg-cagatttttctagatgttctgaatacacataattgatcatatttcttgccatggccacttgcttttgcag
 |||| ||  | ||  | ||    || ||  |  | ||||| ||||| || ||||| || |||||||||||||||||||| ||||| || | ||| ||||||| ||  |   ||||   | |||   |||| |   |   | |   || |  | |||    ||||  ||| ||        || || |||                   
CTTGTTTTCTTACCATTCCTCGTGGCAGCTATGATTGCTGTCTCTCGTGTTGATGATTATTGGCATCATTGGCAAGATGTGTTTGCTGGAGCTCTAATAGgttagttta--ctgatgccagattgattaaatatttcaataaacccttttcaaagtttctgatacgaatattt--------tttttaccag------------------

upper sequence: GRMZM2G024615_T05 (Zea mays), 5'ss of exon 7
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 5'ss of exon 5
ATTGTGTTTCTGCCTCTTCTTACTGCTGCGCTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaatttg-ataaatattttctaaagaggacgcagatttttctagatgttctgaatacacataattgatcatatttcttgccatggccacttgcttttgcag
||||| || |||||  | |||  ||| || || ||||  ||||||||||| |||||||| |||||||| ||||||||||||||||| || ||| | |||||| |||   ||  | |   ||  ||   || |    |     ||  ||||  | ||    ||  | | | |        | |  | |  || ||     || | ||||
ATTGTTTTCCTGCCCATACTTCTTGCAGCTCTAGTGGGAGTTTCTCGAGTAGATGACTATTGGCATCACTGGCAAGATGTATTTGCCGGAGGTGTAATAGgtctgttttatcagtaccgatgattatgaatggaatctttccttactctacttttttctgatttatacactcttctcagtataattctttgtccttcctctctggcag

upper sequence: GRMZM2G024615_T05 (Zea mays), 5'ss of exon 7
lower sequence: Vv17s0000g03170.t01 (Vitis vinifera), 5'ss of exon 5
ATTGTGTTTCTGCCTCTTCTTACTGCTGCGCTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgta------aaat---ttgataaatattttctaaagaggacgcagattttt-ctagatgttctgaatacacataattgatcatatttcttgccatggcc-acttgcttttgcag------------------------------------
||||| || || ||  | ||||  || || ||||| |  |||||||| ||||||||||| |||||||||||||| ||||| ||||  || ||||| |||||| ||||      ||||   ||  ||    |    |    |  |  |||||   | ||| ||||| ||  |  | ||  |   |   |     ||||| | || || ||    ||                                       
ATTGTATTGCTTCCATTGCTTATGGCAGCTCTTGTTGGAGTTTCTCGTGTGGATGACTATTGGCATCATTGGCAGGATGTTTTTGTTGGAGGTCTCATAGgtatgtactccataaatgaattattacgggtcaattccttattaatcagatgaatgctatatgttatggctttatattctaagtgcaaaacaatgccaagtcccacctggaaatgagattaacatgattgattggacatgttgcattgatgcag

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|37381562|gb|CF627675.1|CF627675
EST:     GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTG
genomic: GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaa ... gcttttgcagGTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTG
EST: gi|211034181|gb|FL478457.1|FL478457
EST:     GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTG
genomic: GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaa ... gcttttgcagGTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTG
EST: gi|78119084|gb|DV537468.1|DV537468
EST:     GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCCTTTT
genomic: GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaa ... gcttttgcagGTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCC-TTTT
EST: gi|149100619|gb|EE186707.2|EE186707
EST:     GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCATTTTGCTATCTACAG
genomic: GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaa ... gcttttgcagGTCTTACAGTTGCTTCATTTTGCTATCTACAG
EST: gi|149099698|gb|EE185747.2|EE185747
EST:     GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTG
genomic: GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaa ... gcttttgcagGTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTG
EST: gi|40287149|gb|CK327541.1|CK327541
EST:     GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTG
genomic: GGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaa ... gcttttgcagGTCTTACAGTTGCTTCATTTTGCTATCTACAGTTTTTTCCATATCCTTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTGTTTCTGCCTCTTCTTACTGCTGCGCTTGTGGCTGTTTCTCGAGTGGATGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtttgtaaaatttgataaatattttctaaagaggacgcagatttttctagatgttctgaatacacataattgatcatatttcttgccatggccacttgcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG