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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgggtcacaaatttatacttgccatgttcttttttggaaaccagttaatagaatgtcacgatagttgaatagtgttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG

Basic information

species Zea mays
transcript GRMZM2G023528_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023528_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g03740.1 (Oryza sativa), 3'ss of exon 3
gtgagtgggtcacaaatttatacttgccatgttcttttttggaaaccagttaatagaatgtcacgatagttgaatagtgttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG
||  ||| | ||||    |    ||    | |||||| || | || || || ||  ||                    |||  || |||| |||||| | || || ||||| ||| |||||||| |||||||||| |||||||| |||||||||||||| |||
gtatgtgagccacagcaattggtttaatct-ttctttctttggaatcaattgatgaaa--------------------gttatttgcagGCCAAAAATCCGGAGGTCAGGAGCTTATTGGAGGACTAGATTGTACTGTCCACCGGAACTTTTTTGGGAGCCAG

upper sequence: GRMZM2G023528_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g03000.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------gtgagtgggtcacaaattt----atacttgccatgttcttttttggaaaccagttaatagaatgtcacgatagttgaatagtgttgctttc-agGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG
                                             |   |    || ||||||    ||| ||   ||| | |     | |||   |   |||   | |||   |       | |      |||| ||| || |||||||| ||||||||||| ||||| ||  | ||||||||||| ||||| ||||| ||||| ||||||
gtgggtgttcctttctttattctgcttgttgaaatgcacctataattcttttaacataaatttttcaatatttttaatgatttaagaagcaaaatggcacataacttttcaaattgaaatgttggaacctttttccagGACAGAAAACAGGTGGGCAGGAACTAGTTGGGGGCCTTGATTGTACAGTTCACCGGAACTTCTTTGGCAGTCAG
















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|6020368|gb|AW065296.1|AW065296
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|71318383|gb|DR795955.1|DR795955
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|91055149|gb|EB165567.1|EB165567
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAGACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|5895630|gb|AW036876.1|AW036876
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|78120474|gb|DV538858.1|DV538858
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|33467208|gb|CF244257.1|CF244257
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|74233030|gb|DT640944.1|DT640944
EST:     GGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: GGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|71437533|gb|DR818583.1|DR818583
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|149073844|gb|EE162166.2|EE162166
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|74233031|gb|DT640945.1|DT640945
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|148986692|gb|EE030480.2|EE030480
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|40303169|gb|CK347556.1|CK347556
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCC
EST: gi|15100467|gb|BI396258.1|BI396258
EST:     TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAG                         GGCAAAAAACAGGGGGGCAGGAACTT
genomic: TGTCTGGGGAACCTGTGCTGGGCTCATCTTTCTTGCAAACAAAGCAGTAGgtgagtgggt ... ttgctttcagGGCAAAAAACAGGGGGGCAGGAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttggaaaccagttaatagaatgtcacgatagttgaatagtgttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG
             agttaat  putative branch site (score: 4)
                                             ttgctttc  putative PPT
               ttaatagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgggtcacaaatttatacttgccatgttcttttttggaaaccagttaatagaatgtcacgatagttgaatagtgttgctttcagGGCAAAAAACAGGGGGGCAGGAACTTGTTGGAGGATTAGATTGTACAGTCCACCGAAACTTTTTTGGGAGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT