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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgagggggtttacgcttgctggtgtatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACATTGTTTAGCAATTTTTATCAGATGA

Basic information

species Zea mays
transcript GRMZM2G126435_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126435_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 12
atatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgag--ggggtttacgctt--gctggtgt-atcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACATTGTTTAGCAATTTTTATCAGATGA---
   |  || |||   ||  ||  |  | ||  |||      | |  | | || |   |||| |||||  |         | |  |   ||| | | |||||||||||||| ||||| || ||||||||||| || || || ||||||||||||||||| || | ||   ||||| | | ||       |   |||   || ||     
---tttttgtatgtagtgtctactgtagtt--ttgtgtttgtcttgtaaacagcataatatgtgatttcgttacaaccaaggtcttgactgatttcatcttgcagCCACACCCTGACGTCAAGCCGATGGCCTACGCGAACAACTTCCTCAGGATGTTCCAGTAACAACATATATCCATATC---CGCCTTCTTTCGCCATATTTTTT

upper sequence: GRMZM2G126435_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 12
--atatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgagggggtttacgcttgctggtgtatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACATTGTTTAGCAATTTTTATCAGATGA--
    |   || |      ||     |  |  |||||  | |  | | ||       ||    |||  ||    | || |    |   | ||  |   |||||||||| |||||||| || || |||||||||||||| ||||||||| |||||||   || |   | || | |   | |      | |    |  ||  ||   
aacaaattttctggtgcattatgactgcatatctttcaatctgtgttatatagggttgacattct--ttccttgtgtctggtttattttgttgaatatgcagCCACACCCTGATGTCAAACCTATGGCATATGCAAACAACTTCCTCCGGATGTTCTCATAATTTA-TACAGCTG-ACTAGAAGCCTAGAACTGCCAATTGTTA

upper sequence: GRMZM2G126435_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 13
---------atatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatat---ctgattgagggggtttac--gcttgctggtgt----atcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGAC-GGAATATAACAACATTGTTTAGCAATTTTTATCAGATGA
          |   |||  ||    ||  | |||    | |||      |  |  ||  |   | ||| |   || ||| |     | | |    || ||| | |    || |  ||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||||||  | | ||  | | | | |  | |    |   |||  |  ||  | | 
gtgagtgtagtcctcttacatagcattgttcttatgaatgtttcacagaagatagttcacggtttgatttagactcattcaaacactcttctaattttctgatattgttatttcccagCCTCATCCGGATGTGAAGCCTATGGCATATGCAAACAACTTTCTCAGGATGTTCAACTAACCAGCAAAAAGCTTCTTCTACTCAAAATGCTATTCTAAAG-

upper sequence: GRMZM2G126435_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 6
-----------atatccttttatc-atgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgagggggtttacgcttgctggtgt-atcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACA-TTGTTTAGCAATTTTTATCAGATGA
            | |  | | |   ||  | ||| |||| ||  |      | ||| ||       |  |  | | | |       ||    |||  ||   | |  ||||||||||| |||||||||||||| ||||| ||||| |||||||| ||| |||||||    |||  |  | || |  || |||| |  ||||||||   | |  |
gtgagtagcctgtgttttctgaaagatccttctgctaaattttgtcaacttggttt-atagatggttaaaagtgtaacttgtcctcttatttctttttgtgatgaaattgcagCCACACCCTGATGTGAAGCCAATGGCGTATGCCAATAACTTTCTCCGGATGTTCTCTTGATTGG-TGTACCGCCAGTTGTATGTCAATTTTTTCTATACAA

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|60397240|gb|DN230056.1|DN230056
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTTTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|32908873|gb|CF013686.1|CF013686
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|32793545|gb|CD945781.1|CD945781
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|37375420|gb|CF624146.1|CF624146
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|88747125|gb|DY531266.1|DY531266
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTTTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAA-TAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|31362995|gb|CD447352.1|CD447352
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTTTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|78543587|gb|DV621085.1|DV621085
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|31362555|gb|CD446912.1|CD446912
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|67010423|gb|CO439172.1|CO439172
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|149082014|gb|EE171184.2|EE171184
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|5069750|gb|AI737715.1|AI737715
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|71319055|gb|DR796273.1|DR796273
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|71769983|gb|DR967920.1|DR967920
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTTTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|166548079|gb|EG301575.1|EG301575
EST:     AGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTAG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCA
genomic: AGAAATGAAACCAGATATTGTTACTTTCTCAGCTGT-Ggtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCA
EST: gi|211035490|gb|FK976709.1|FK976709
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|32907203|gb|CF012016.1|CF012016
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|17970082|gb|BM276848.1|BM276848
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGGTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|61118887|gb|DN559848.1|DN559848
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACT
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACT
EST: gi|101392445|gb|EB818152.1|EB818152
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTTTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|211002184|gb|FL463664.1|FL463664
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|17921945|gb|BM259596.1|BM259596
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|37382436|gb|CF628164.1|CF628164
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|91877631|gb|EB407588.1|EB407588
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTTTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|84977182|gb|DW475604.1|DW475604
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|37398928|gb|CF636784.1|CF636784
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|60400166|gb|DN232973.1|DN232973
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|149082499|gb|EE171692.2|EE171692
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
EST: gi|32868068|gb|CF007750.1|CF007750
EST:     GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTG                         CCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG
genomic: GCTTCACAGCTCCAGAAATGAAACCAGATATTGTTACTTTCTCAGCTGTGgtgagtagtt ... tatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagcaactggatatctgattgagggggtttacgcttgctggtgtatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACATTGTTTAGCAATTTTTATCAGATGA
              atctgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatccttttatcatgttcctgttaaacttctttgcaccgatttgattagcaactggatatctgattgagggggtttacgcttgctggtgtatcttgcagCCACATCCTGATGTGAAGCCGATGGCATATGCAAATAACTTCCTCAGGATGTTTCAATGACGGAATATAACAACATTGTTTAGCAATTTTTATCAGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - catgttc
- - - - - - - - - - - - - - - ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - -gcaactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctggtg