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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacctacatcgttgtacttgtacaagaccgagacgataggttttgtctgttgaaacgggaatgtgatgtttacgaataacctctgttcgtttccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTCGCCAAGGAGCCGTTCGAGGTCAAGTCCGGCTCCTGTGGCACCGTCGTCA

Basic information

species Zea mays
transcript GRMZM2G055320_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055320_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g44620.2 (Oryza sativa), 3'ss of exon 2
gcacctacatcgttgtacttgtacaagaccgagacgataggt--tttgtctgttgaaacgggaatgtgatgtttacgaataacctctgttcgttt--ccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTCGCCAAGGAGCCGTTCGAGGTCAAGTCCGGCTCCTGTGGCACCGTCGTCA
  |||      ||   |||   ||      || |     | |  ||       |||| ||   |     |   | |   |    | | ||  |||  |   |||||||| |||||||| ||||| || || |||||||||||||| ||||||||||| |||||||| |||||||||||||||||||| || || || |||||||
--accgtgg--gtgacactgacactgatgtgaaatttctgatccttaagtgactgaatcgctgagaaattcactgcatttcgtttttttttctttttctgacagGGGTATGGGATGACTGAGGCTGGACCTGTGCTGGCCATGTGTCTGGCCTTCGCAAAGGAGCCATTCGAGGTCAAGTCCGGCTCGTGCGGGACAGTCGTCA

upper sequence: GRMZM2G055320_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0052g01090.t01 (Vitis vinifera), 3'ss of exon 1
-------gcacctacatcgttgtacttgtacaagaccgagacgataggttttgtctgttgaaacgggaatgtgatgtttacgaataacctctgttcgtttccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTCGCCAAGGAGCCGTTCGAGGTCAAGTCCGGCTCCTGTGGCACCGTCGTCA
            |||    |||| | || |   | || |||  ||   |    ||  |       |||  |    |  ||  | |    | | | | | |    ||||| ||||||||||| |||||||| |||||| |||| |||||| ||||||| ||||| ||||| |||||| ||||||| || || |||||||| || ||||
ttttacgctttttacccaattgtccatgcatttgtccaaga-aattcataaaatcctt------aggagggctgagggtaaaattggaatgtttgcatgtatggcagGGCTACGGGATGACAGAGGCGGGACCCGTGTTGGCAATGTGCTTGGCCTTTGCCAAAGAGCCATTCGAGATCAAGTCTGGGTCTTGTGGCACAGTGGTCA
















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|6587590|gb|AW244908.1|AW244908
EST:     ACCTCCAGGACGCGTTCATGGCCAAGATCCCCAACGCCGTGCTCGGCCAG                         GGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTC
genomic: ACCTCCAGGACGCGTTCATGGCCAAGATCCCCAACGCCGTGCTCGGCCAGgtctgttcgc ... tttccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTC
EST: gi|76911497|gb|DV164299.1|DV164299
EST:     ACCTCCAGGACGCGTTCATGGCCAAGATCCCCAACGCCGTGCTCGGCCAG                         GGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTC
genomic: ACCTCCAGGACGCGTTCATGGCCAAGATCCCCAACGCCGTGCTCGGCCAGgtctgttcgc ... tttccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTC
EST: gi|76924616|gb|DV170051.1|DV170051
EST:     ACCTCCAGGACGCGTTCATGGCCAAGATCCCCAACGCCGTGCTCGGCCAG                         GGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTC
genomic: ACCTCCAGGACGCGTTCATGGCCAAGATCCCCAACGCCGTGCTCGGCCAGgtctgttcgc ... tttccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgttgaaacgggaatgtgatgtttacgaataacctctgttcgtttccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTCGCCAAGGAGCCGTTCGAGGTCAAGTCCGGCTCCTGTGGCACCGTCGTCA
                             gaataac  putative branch site (score: 2)
                                   cctctgttcgtttcc  CT-rich tract
                     atgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacctacatcgttgtacttgtacaagaccgagacgataggttttgtctgttgaaacgggaatgtgatgtttacgaataacctctgttcgtttccaccagGGGTACGGGATGACCGAGGCGGGGCCCGTGCTGGCCATGTGCCTGGCCTTCGCCAAGGAGCCGTTCGAGGTCAAGTCCGGCTCCTGTGGCACCGTCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - ctacatc
- - - - - - - gtacttg
- - - - - - - - - - - - - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt