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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatacagagaattgtcaagtccattaactacttttaaactcttgtgatagagtactgaccattcatttgatgattgtttcttatattctcaactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCT

Basic information

species Zea mays
transcript GRMZM2G083344_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os05g15160.1 (Oryza sativa), 3'ss of exon 8
---ggatacagagaattgtcaagtccattaactacttttaaactcttgtgatagagtactgaccattcatttgatgattgtttcttatattctcaactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCT
      |     || || | ||||||   |  ||| |||||| ||   | |   | ||      | |    || ||||| ||| | | |  |  |  || |||||||||||||||||| ||||||||||||| || |||||||| ||||| |||||||||||| |||||||| |||||||| |  ||||||||||||| ||||
gccctttctcatgatttcttaagtccgcaagatacctttaaagtcacct-acgcattatcattgactttcatgttgattctttataaca--caaattttgcagATTGAAGGACCTCAACTAGTGCAGCATGGATTCAAAGATGCTATTGCTAAAGTTGGATTAGCAAAGTTGGTTTCTAATCTCCTTGTGGTGGGCTTGTTCT
















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|8665718|gb|BE186534.1|BE186534
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|71760100|gb|DR958037.1|DR958037
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|32928246|gb|CF033058.1|CF033058
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|32165070|gb|CD670388.1|CD670388
EST:     TTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: TTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|71328475|gb|DR800887.1|DR800887
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|76930049|gb|DV172255.1|DV172255
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|71768355|gb|DR966292.1|DR966292
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|32935156|gb|CF039968.1|CF039968
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|32862760|gb|CF002442.1|CF002442
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
EST: gi|166466843|gb|EG171627.1|EG171627
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGC
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGC
EST: gi|32837170|gb|CD976848.1|CD976848
EST:     CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATT                         ATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA
genomic: CATACATATCAATAATTGCTCTCTTTGTCTGCATCCCCCCTGCAATTATTgtaagcctag ... caactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagagtactgaccattcatttgatgattgtttcttatattctcaactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCT
                                tttcttatattctc  CT-rich tract
                            attgtttcttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatacagagaattgtcaagtccattaactacttttaaactcttgtgatagagtactgaccattcatttgatgattgtttcttatattctcaactttcagATTGAAGGACCTCAATTAGTGCAGCATGGTTTTAAAGATGCAATTGCCAAAGTTGGATTAACAAAGTTGATTTCTAATTTTTTTGTGGTGGGCTTATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgatg