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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcagcgaattatattattcctctgatgtttgagccatccgtgtgatgtgtggttgtagactatattacatgctgtttattgtttgtagcctgatggtgtctatgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGCAATGTGCACGGTGTGAACCCCAAGTTTCTGGAGGTTGGAGAGAGGATAG

Basic information

species Zea mays
transcript GRMZM2G175453_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g05990.1 (Oryza sativa), 3'ss of exon 5
-----------------gtactcagcgaattatattattcctctgatgtttgagccatccgtgtgatgtgtggttgt----agactatattacat-gctgtttattgtttgtagcctgatggtgtctatgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGCAATGTGCACGGTGTGAACCCCAAGTTTCTGGAGGTTGGAGAGAGGATAG
                 ||   ||  |    |   |     | ||| ||||    |||     | | |  |   | |    | | ||| | |  | | || || |  ||  |   ||||||||     | | | |||| | ||||| |||||||| || || |||||||| |||||||| | |||||||||||| || ||||| || ||||||||||| |||||||||||||| || |
gtactcaattaagtagggtctgcaatgttcaagtgtgacagtgtgaagtttctatcatgtagctaacgcataagtattcaaaaattatgtaatttagttgattttccttactgagctgatggt--tggtacaacgtagGTTTTGCGACTGTCAGGAGCTACACAAGATCTCCCCAAGTCCATGATCTGCAATGTACATGGTGTCAATCCCAAGTTTCTTGAGGTTGGAGAGAGAATTG

upper sequence: GRMZM2G175453_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0105g00260.t01 (Vitis vinifera), 3'ss of exon 5
gtactcagcgaattatattattcctctgatgtttgagccatccgtgtgatgtgtggttgtagactatattacatgctgtttattgtttgtagcctgatggtgtcta--tgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGCAATGTGCACGGTGTGAACCCCAAGTTTCTGGAGGTTGGAGAGAGGATAG
              | ||  |     | || |||   ||| | || | |  | ||  |  | || |||    |  || || ||  |   || |   || |  |||     ||||  || |  | || || || | ||| || || ||  | ||||||||    || |||||||| |||||||||||||||||||||||| |  |||||||||   | |
-------------gagatggtctaagtaattttt---ccaacagttttacctttgaattcaaac-atacgggac-cttttcatattcattaactaaattgcatctgatctctatccagGTTCTTCGCCTTTCGGCTGCTACCCAGGACTTACCCAAGTCTGTAATTTGCAATGTTCACGGTGTGAACCCCAAGTTTCTGAAAATTGGAGAGAAACTGG
















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|13237069|gb|BG355083.1|BG355083
EST:     TTTTCGTTAAGCACATTAATAACCTGGTCGCCAGAGCTTATTGCCATAAG                         ATCTTGCGGCTGTCAGGTGCCACTCAAGAACTTCCCAAGTCGACGATCTGC
genomic: TTTTCGTTAAGCACATTAATAACCTGGTCGCCAGAGCTTATTGCCATAAGgtactcagcg ... tgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGC
EST: gi|91872681|gb|EB402638.1|EB402638
EST:     TTTTCGTTAAGCACATTAATAACCTGGTCGCCAGAGCTTATTGCCATAAG                         ATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGC
genomic: TTTTCGTTAAGCACATTAATAACCTGGTCGCCAGAGCTTATTGCCATAAGgtactcagcg ... tgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGC
EST: gi|13237254|gb|BG355268.1|BG355268
EST:     TTTTCGTTAAGCACATTAATAACCTGGTCGCCAGAGCTTATTGCCATAAG                         ATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGC
genomic: TTTTCGTTAAGCACATTAATAACCTGGTCGCCAGAGCTTATTGCCATAAGgtactcagcg ... tgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactatattacatgctgtttattgtttgtagcctgatggtgtctatgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGCAATGTGCACGGTGTGAACCCCAAGTTTCTGGAGGTTGGAGAGAGGATAG
                              gcctgat  putative branch site (score: 4)
                 tttattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcagcgaattatattattcctctgatgtttgagccatccgtgtgatgtgtggttgtagactatattacatgctgtttattgtttgtagcctgatggtgtctatgctatgtagATCTTGCGGCTGTCAGGTGCCACTCAAGATCTTCCCAAGTCGACGATCTGCAATGTGCACGGTGTGAACCCCAAGTTTCTGGAGGTTGGAGAGAGGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT