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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttcgcacataaattatgggctactttatctaatggtctatgtagtttattgttccatcaattctgttcgaactcacaccccaacctctaattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAATTATCCTTTCCGAACAAAATGCAATCGTCCCCAATGTGGAGCAGAAAA

Basic information

species Zea mays
transcript GRMZM2G107106_T06
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107106_T06 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 8
attttcgcacataaattatgggctactttatctaatggtctatgtagtttattgttccatc--aattctgttcgaactcacaccccaacctctaattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAATTATCCTTTCCGAACAAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
         ||||| ||||| |   |  |    | | ||   |||| |   ||  ||| |   |||||| |   | ||      | ||  | | || |  |||| ||||||||||||| || ||||||||||| ||| |||||||||||||||| ||||| ||||| |||||||| || |||||    || |  || |||||
-ccacattgcataagttatgcgtgtcacttagcactagttcttgtaatggctttgtcctttttaattctatataatctttacatctaatatttcat-ggcagAACCAAAGATGCCAGAAGGTAGTTGGAAGTGCGAGAAGTGCAATAACATAAACTATCCATTCCGCACAAAATGTAACCGTCCAAGTTGCGAGGCTGAAAA

upper sequence: GRMZM2G107106_T06 (Zea mays), 3'ss of exon 7
lower sequence: Vv01s0010g03700.t01 (Vitis vinifera), 3'ss of exon 8
attttcgcacataaattatgggctactttatctaatggtctatgtagtttattgttccatcaattctgttcgaactcacaccccaacctctaattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAATTATCCTTTCCGAACAAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
                  || | | |||| |  | | |    | |  ||   | || ||| || | || |    || |||    |  |  | |||   ||||  ||||||||| || || ||||||||||||||| |||| |  |||||||| ||||| ||| |||| || |||||| | |   | ||||| || || ||
-----------------gtgagtt-cttttttaacttgctgctattattggct-ttgcattaactttgat---gctaacata--attcatttatt--cagAACAAAAGATGCCTGATGGAAGTTGGAAGTGTGAGAAGTGTAGCAACATAAACTATCCCTTCAGAACCAAGTGCAATAGACAGAACTGTGGGGCCGATAA
















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|32929362|gb|CF034174.1|CF034174
EST:     GGATCTAAGTCTGATGGTTTAAGGGGCTCAA                         AAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|38502536|gb|CF972396.1|CF972396
EST:     GGATCTAAGTCTGATGGTTTAAGGGGCTCAA                         AAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|60354809|gb|DN221782.1|DN221782
EST:     GGATCTAAGTCTGATGGTTTAAGGGGCTCAA                         AAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|71765407|gb|DR963344.1|DR963344
EST:     GGATTTAAGTTTGATGGTTTAAGGGGCTC--                         AA-CAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|71760238|gb|DR958175.1|DR958175
EST:     GGATCTAAGTCTGATGGTTTAAGGGGCTCAA                         AAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|32929980|gb|CF034792.1|CF034792
EST:     GGATCTAAGTCTGATGGTTTAAGGGGCTCAA                         AAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|86469486|gb|DY235856.1|DY235856
EST:     GGATCTAAGTCTGATGGTTTAAGGGGCTCAA                         AAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|60336833|gb|DN203806.1|DN203806
EST:     GGATCTAAGTCTGATGGTTTAAGGGGCTCAA                         AAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
EST: gi|71761651|gb|DR959588.1|DR959588
EST:     GGATCTAAGTTTGATGGTTTAAGGGGCTCAA                         AAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA
genomic: GGATCTAAGTCTGATGGTTTAAGGGGCTCAAgtaagtttcc ... taattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttattgttccatcaattctgttcgaactcacaccccaacctctaattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAATTATCCTTTCCGAACAAAATGCAATCGTCCCCAATGTGGAGCAGAAAA
                                         cctct  CT-rich tract
                                             taattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttcgcacataaattatgggctactttatctaatggtctatgtagtttattgttccatcaattctgttcgaactcacaccccaacctctaattgatagAAGCAAAGATGCCAGAGGGCAGTTGGAAGTGTGAGCAGTGCAATAACATAAATTATCCTTTCCGAACAAAATGCAATCGTCCCCAATGTGGAGCAGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG