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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagctgcaatattatgatatttttaatatattttatttatacaatgctatcgggagtgactcttgtttgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACAGATGGGTCCTGGTGGTTTATTTTTTACCGGGGATGGAACTGGTGAGCTC

Basic information

species Zea mays
transcript GRMZM2G037200_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037200_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g45480.3 (Oryza sativa), 3'ss of exon 4
gtaagcaagctgcaatattatgatatttttaatatattttatttatacaatgctatcgggagtgactcttgtttgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACAGATGGGTCCTGGTGGTTTATTTTTTACCGGGGATGGAACTGGTGAGCTC
||||| ||| ||   |  || |||  ||||      ||||| || |    |  |||| | |||| ||| | || | ||| |||||||||||| || |||||  ||||||| ||| | ||||| |||||||||||  | |||||| |||||||||||||||| |||||||||||||||||||| 
gtaagaaagttgtcttgctaagattattttg-----ttttacttctgatgt-ttatctgaagtggctccttttgggtttgtagGTTCAGTGATAGGGGCAGGATATTCTCAAAACAGGAAATAAGGGCAATACAAGTTGGTCCTAGTGGTTTATTTTTTACTGGGGATGGAACTGGTGAGCTG
















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|60345951|gb|DN212924.1|DN212924
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|6020641|gb|AW065674.1|AW065674
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|60347714|gb|DN214687.1|DN214687
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|71429256|gb|DR810306.1|DR810306
EST:     CTTCTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|29576813|gb|CB616925.1|CB616925
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|149070981|gb|EE159386.2|EE159386
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|149086360|gb|EE175901.2|EE175901
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|50334152|gb|CO529278.1|CO529278
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|149095549|gb|EE181206.2|EE181206
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|211495269|gb|FL457209.1|FL457209
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|60344000|gb|DN210973.1|DN210973
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|88751062|gb|DY535203.1|DY535203
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|31997695|gb|CD661718.1|CD661718
EST:     CTACTGTGTTCATTAAATGACAACNCTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|5847063|gb|AW000142.1|AW000142
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|78074602|gb|DV503036.1|DV503036
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
EST: gi|71297927|gb|DR784933.1|DR784933
EST:     CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATC                         GTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA
genomic: CTACTGTGTTCATTAAATGACAACACTGTCCGCTTATATGATCTGCCATCgtaagcaagc ... tgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatatattttatttatacaatgctatcgggagtgactcttgtttgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACAGATGGGTCCTGGTGGTTTATTTTTTACCGGGGATGGAACTGGTGAGCTC
 ttttaat  putative branch site (score: 3)
                                     ctcttgtttgtttt  putative PPT
     atattttatttataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaagctgcaatattatgatatttttaatatattttatttatacaatgctatcgggagtgactcttgtttgttttatagGTTCAGTGACAGAGGCAGATTATTCTCCAAAAAAGAAATTAGGGCAATACAGATGGGTCCTGGTGGTTTATTTTTTACCGGGGATGGAACTGGTGAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA