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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggttgcttcatttcttgtcaatctttctgtttgtatgtgcttattttcatagttttacaatgtacctatttcttagtctcacgaaggcacagcttgtagGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCATCTGTAGAATGGGGCATTCCGGTGCCAAACGATACCAAGCAGACAATAT

Basic information

species Zea mays
transcript GRMZM2G029055_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 4
gggttgcttcatttcttgtcaatctttctgtttgtatgtgcttattttcatagttttacaatgtacctatttcttagtctcacgaa--ggcacagcttgtagGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCATCTGTAGAATGGGGCATTCCGGTGCCAAACGATACCAAGCAGACAATAT
    |  |   ||| | | || |||||| || || || || || || |    |||||  ||| ||  | ||  |||  ||  |  |     |||| |||||||||||||| ||| ||||||| |||||||||||||| |||||||| |||||||||||||| ||||| |||||||||||||| || ||||| ||||||||||
-atatcatatgtttatggacagtctttcagtatgcatatgatttttgtttgtgttttcaaatatagttgttctttaccctttctgattaagacag-ttgtagGTCCAAGGATGGGTTAAAAGTGGATTAAGGGACTTCTCTATTTCCCGTGCATCTGTAGAGTGGGGTATTCCGGTGCCAAATGACACCAAACAGACAATAT

upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0019g00810.t01 (Vitis vinifera), 3'ss of exon 4
gggttgcttcatttctt---gtcaatctttc-tgtttgtatgt---gcttattttcatagttttacaatgtacctatttcttagtctcacgaaggcacagcttgtagGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCATCTGTAGAATGGGGCATTCCGGTGCCAAACGATACCAAGCAGACAATAT
      ||| |  | |    | || |||||  ||| |  ||||   | | |   |     |  | |  | |  | || | |   |      |  | ||  ||  ||||| ||| | ||||| ||||| ||  | ||||| ||||||||||| || |||||||| || ||||||||||| || || || || | ||||||||| ||||
------cttgaaatttaaaagacattctttaatgtattaatgtaaggttcacactaccgatgctgctttctttcaatatatcgcttctgatatagaacttctc-tagGTGCAAAGTTGGATCAAAAGTGGTCTGAGGGATTTTTCTATTTCCCGAGCATCTGTGGATTGGGGCATTCCTGTTCCTAATGACAACAAGCAGACCATAT
















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|148964149|gb|EE015315.2|EE015315
EST:     TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAG                         GTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCA
genomic: TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAGgtgaggtttt ... cagcttgtagGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCA
EST: gi|148957317|gb|EC903360.2|EC903360
EST:     TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAG                         GTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCA
genomic: TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAGgtgaggtttt ... cagcttgtagGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCA
EST: gi|149076722|gb|EE165367.2|EE165367
EST:     TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAG                         GTCCAAGGCTGGGAT-AAAAGCGGATTAAGGGACTT
genomic: TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAGgtgaggtttt ... cagcttgtagGTCCAAGGCTGG-ATTAAAAGCGGATTAAGGGACTT
EST: gi|78110212|gb|DV528627.1|DV528627
EST:     TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAG                         GTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCA
genomic: TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAGgtgaggtttt ... cagcttgtagGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCA
EST: gi|78086927|gb|DV515320.1|DV515320
EST:     TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAG                         GTCCAAGGCTGGATTAAAAGC
genomic: TACTGACAAGAAATCCTGATTTTGTAAGGCCATCATATCGCTTGAACGAGgtgaggtttt ... cagcttgtagGTCCAAGGCTGGATTAAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatagttttacaatgtacctatttcttagtctcacgaaggcacagcttgtagGTCCAAGGCTGGATTAAAAGCGGATTAAGGGACTTTTCTATTTCTCGTGCATCTGTAGAATGGGGCATTCCGGTGCCAAACGATACCAAGCAGACAATAT
                               gtctcac  putative branch site (score: 3)
        ttttacaat  TA-rich tract