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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattagttcaatgcacaaatactgcacatttgcacccactgctcaatgcttgtggtatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAG

Basic information

species Zea mays
transcript GRMZM2G158627_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158627_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g43760.1 (Oryza sativa), 3'ss of exon 19
gtatgattagttcaatgc---acaaatactgcacatttgc--acccactgctcaatgcttgtggtattt-cttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAG
|||||  ||  | |  ||   | |||   ||||  |||    | | ||||||||   |||||| ||||| ||||||||||| ||||||||||| |||||||||||||||||||| |||||||  |||||||| ||||| |||||||||||||||| ||| ||| |||||||||| 
gtatgtgtacctaatagcgtgagaaactttgcatttttttttatctactgctcagcacttgtgttattttcttagTGTGCTAGGAAAAAGACTGGGAAAGGACATGGGCAAAGTGTCAAATGAAGTGAAGAAAATGACACAGGAACAGATCTTAGCCTTTGAACAAAGTGGAGAA
















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|20208226|gb|BQ134315.1|BQ134315
EST:     TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGAC
genomic: TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGAC
EST: gi|87156879|gb|DY401668.1|DY401668
EST:     TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGACTTGG
genomic: TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGACTTGG
EST: gi|67025030|gb|CO453779.1|CO453779
EST:     TGCAATGACCCCTTGATTTATGCCTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
genomic: TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
EST: gi|32933872|gb|CF038684.1|CF038684
EST:     TGCAATGACCCCTTGATGTATACTTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
genomic: TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
EST: gi|74240586|gb|DT648500.1|DT648500
EST:     TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
genomic: TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
EST: gi|32934686|gb|CF039498.1|CF039498
EST:     TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
genomic: TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
EST: gi|26456279|gb|CA827862.1|CA827862
EST:     ACCCCTTGATGTATGCTTTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
genomic: ACCCCTTGATGTATGC-TTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
EST: gi|32932327|gb|CF037139.1|CF037139
EST:     TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAATATCAAATGTGGT
genomic: TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
EST: gi|71432888|gb|DR813938.1|DR813938
EST:     TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAG                         TGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT
genomic: TGCAATGACCCCTTGATGTATGCTTCTCTGCGAGCTGAACCTAATTTCAGgtatgattag ... tatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcacaaatactgcacatttgcacccactgctcaatgcttgtggtatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAG
                                             tatttctt  CT-rich tract
                                             tatttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgattagttcaatgcacaaatactgcacatttgcacccactgctcaatgcttgtggtatttcttagTGTGCTGGGAAAAAGACTTGGAAAGGACATGGGCAAAGTATCAAATGTGGTGAAGAAGATGACTCAGGAACAGATCTTAGACTTCGAAAAAAGTGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA