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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttccaatgcctcctctagttcaattttagatgccttgatctaatgtatattggtggatttcttacatgctcccagctgatactagttactacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGGACATTCGATCTGAGGGTTCTCTTGATTCTGCTGATCGGTGTGCCAATCC

Basic information

species Zea mays
transcript GRMZM2G079682_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079682_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g38140.2 (Oryza sativa), 3'ss of exon 1
ctttccaatgcctcctctagttcaattttagatgccttgatctaatgta-tattggtggatttcttacatgctcccagctgatactagttact-acttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGGACATTCGATCTGAGGGTTCTCTTGATTCTGCTGATCGGTGTGCCAATCC
|  |  | ||        |     || | |      | | | |  | |  | |  || ||   | |   |  || ||  || |    |  | | | ||||||| |||||||||| || | ||||||||||| ||| ||||||| ||||| |||   || ||| ||||||  ||  |||| ||  |||| |||||||||   |
cagttgattggtgttgaaataattatgtgaagaagatgggtttcttttggtttcagttgacagcctgatt--tctcacttgttttctgaaattcatttgcagCATGGTTCAAAGGCAATTCTGAGCATGTCAAGGTTGAAGTGTGCGCTTCGGGGGTTTGATTTGAGGGCACTTCTGATCCTCTTGATTGGTGTGCCAGCTC
















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|86466341|gb|DY232712.1|DY232712
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|86466341|gb|DY232712.1|DY232712
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71770961|gb|DR968898.1|DR968898
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71770961|gb|DR968898.1|DR968898
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|149098671|gb|EE184680.2|EE184680
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|149098671|gb|EE184680.2|EE184680
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|76926193|gb|DV170756.1|DV170756
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|76926193|gb|DV170756.1|DV170756
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|149105738|gb|EE291314.2|EE291314
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|149105738|gb|EE291314.2|EE291314
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|78078055|gb|DV506470.1|DV506470
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         CTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGG
EST: gi|71432765|gb|DR813815.1|DR813815
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71432765|gb|DR813815.1|DR813815
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|148989949|gb|EE031822.2|EE031822
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|148989949|gb|EE031822.2|EE031822
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|149105856|gb|EE291458.2|EE291458
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|149105856|gb|EE291458.2|EE291458
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|149102165|gb|EE287589.2|EE287589
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|149102165|gb|EE287589.2|EE287589
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|148931731|gb|EC874964.2|EC874964
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|148931731|gb|EC874964.2|EC874964
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71312923|gb|DR792984.1|DR792984
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71312923|gb|DR792984.1|DR792984
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71447556|gb|DR828606.1|DR828606
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71447556|gb|DR828606.1|DR828606
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|78086273|gb|DV514666.1|DV514666
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|78086273|gb|DV514666.1|DV514666
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|148957087|gb|EC903057.2|EC903057
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|148957087|gb|EC903057.2|EC903057
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71767841|gb|DR965778.1|DR965778
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71767841|gb|DR965778.1|DR965778
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71449434|gb|DR830484.1|DR830484
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71449434|gb|DR830484.1|DR830484
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|50328019|gb|CO523145.1|CO523145
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|50328019|gb|CO523145.1|CO523145
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|71430357|gb|DR811407.1|DR811407
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|71430357|gb|DR811407.1|DR811407
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAGCGA                      
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCG--A-C-Agcgaggtgag ... ctacttg
EST: gi|78106713|gb|DV525131.1|DV525131
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-
EST: gi|78106713|gb|DV525131.1|DV525131
EST:     CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACA                         G
genomic: CTACTGCAACCGCAAGAAGACCGACGGCATCTGCGACGGCGTCTGCGACAgcgaggtgag ... ctacttgcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatattggtggatttcttacatgctcccagctgatactagttactacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGGACATTCGATCTGAGGGTTCTCTTGATTCTGCTGATCGGTGTGCCAATCC
             atttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttccaatgcctcctctagttcaattttagatgccttgatctaatgtatattggtggatttcttacatgctcccagctgatactagttactacttgcagCTTGGTTCAAAGTCAGTCCTGAGCATGTCGAGGCTGAAGTGCGCGCTGCGGACATTCGATCTGAGGGTTCTCTTGATTCTGCTGATCGGTGTGCCAATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - tgcctcc
- - - - - - - - - - - - - - - - tgccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgata