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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagttgacagcatttttttatcaaaatgatatttttgatctttctttgcatcccaatattacctcagaagtcagaaatgtaagctgctaacctattgcagGTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGATCATGAGGTTCGTCTGTGGGATGCTAATACTTCAGACTGTATTGGATCAC

Basic information

species Zea mays
transcript GRMZM2G353548_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G353548_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 5
---tagttgacagcatttttttatcaaaatgatatttttgatctttctttgcatcccaatattacctcagaagtcagaaatgtaagctgctaacctattgcagGTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGATCATGAGGTTCGTCTGTGGGATGCTAATACTTCAGACTGTATTGGATCAC
    ||        || | |||  || ||  ||   |     || | ||||||  |  || |  |        |    | | |   || ||   ||||| ||||| || |||||||| |||| | |||| || || ||||| || ||||||||||| || || ||||| ||||| ||||| || ||||||||||||||||| |
agggagcattttatatatgttttacataaaaatgcataaatgctgtttttgcagtcttatttgccacttattattttgagttt---cttctgttctatttcagGTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGATCAGGAAGTCCGTCTTTGGGACGCTAAAACCTCAGACTGTATTGGATCTC

upper sequence: GRMZM2G353548_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 4
---tagttgacagcatttttttatcaaaatgatatttttgatctttctttgcatcccaatattacctcagaagtcagaaatgtaagctgcta-acctattgcagGTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGATCATGAGGTTCGTCTGTGGGATGCTAATACTTCAGACTGTATTGGATCAC
    | ||  || |||| |   |   |||| |        | || ||||     | |||  |  | ||     ||          |||| |  | || ||  |||| || |  |||||  |  || |||| || || || |||||||||||||||||||| |||||  |||||||||| | |||| |||| || || || ||||
ccccaattagcatcattctaacaatgaaatcaagaaaagaaactctctt----actcaaggtagcttcttctttccatctgacgtgctggtggaacttttatagGTTAGATTTCATCCACTCTATCCTGAAATACTTGCAAGTGGAAGTTTGGATCATGAAGTTCGATTGTGGGATGCAAGTACTGCAGAGTGCATAGGGTCAC
















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|28873754|gb|CB329699.1|CB329699
EST:     CAGGGAAATGTGTGAAGGTTTTGAGTGGACATCGACGCACTCCTTGGGTG                         GTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGAT
genomic: CAGGGAAATGTGTGAAGGTTTTGAGTGGACATCGACGCACTCCTTGGGTGgtatgtctat ... cctattgcagGTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGAT
EST: gi|78106525|gb|DV524943.1|DV524943
EST:     CAGGGAAATGTGTGAAGGTTTTGAGTGGACATCGACGCACTCCTTGGGTG                         GTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGAT
genomic: CAGGGAAATGTGTGAAGGTTTTGAGTGGACATCGACGCACTCCTTGGGTGgtatgtctat ... cctattgcagGTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatcccaatattacctcagaagtcagaaatgtaagctgctaacctattgcagGTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGATCATGAGGTTCGTCTGTGGGATGCTAATACTTCAGACTGTATTGGATCAC
                                       tgctaac  putative branch site (score: 1)
         aatatta  TA-rich tract