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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtatttatttgagattaatcgattcattttatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG

Basic information

species Zea mays
transcript GRMZM2G038848_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 9
------------------gttcgtatttatttgagatta--atcgattcatt--ttatatatctgtttcaacatcaaatga--tttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
                     |||| |    |   ||    |   ||| | |  || ||||||||     |   | | | |   ||  |||||||  |||||||   |||||||||||| || ||||| || |||||||||||||| || ||||| || |||||||||||||| |||| | |||| || ||||
gcatgtaacttgagatactgacgtactgtactactatggctacaaatttagtggttgtatatctgccatgattactagtcaatctttctctctaatgcatgcatttgtgtagGACGTGGAGCGAAGGAGGCGAATCTTTACACTGAGATAGCTGAAGGCATCCATGCTTATGGAATAAAAGGCCACCGTCATG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------gttcgtatttatttg-agattaatcgattcat-tttatatatctgtt-tcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
                                                 |   ||| ||| |  | ||  ||  ||  || | ||||||| ||   |||  || |  |||| || | | ||| ||||| ||  ||||||||||||| ||||||||||| ||||| ||||| || || ||||| || || ||||||||||| |||| | |||| |||||||
gtatgcattttgcatgagatactctgactattaagtaattatatatatatatatatatatatatatatatatatatatatatatatatatatgccatcattattagctgatatgctgtgtaacacatgtatt-ttgtagGACGTGGAGCTAAGGAAGCCAATCTCTACACCGAGATAGCTGAAGGCATTCATGCTTATGGAATAAAAGGCCACCGGCATG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT2G19940.1 (Arabidopsis thaliana), 3'ss of exon 9
gttcgtatttatttgagattaatcgattcattttatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
           |||||| ||| ||  |      |  | |  || | |||  |    |  |||  |  || | |      |      ||||||||| |||||||| |||||||||||| |||| || ||||| || ||   | |||||||  | ||  | ||||| ||||
----------gtttgagcttactccgtgatcaatgaacaa-tgatgcaatgtttc-tagtttcttgactgatatgaaattttcatcagGACGTGGTGCTAAGGAGGCAAATCTTTACTCTGAGATAGCTGAAGGCATTTCTTCTTATGGTGTCACCCGTCATCGCCATG

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 8
----------gttcgtatttatttgagat-taatcgatt--cattttatatatctgtttcaacatcaaatg-attt----ggtctctaaaacatgcatcatt--gtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
           ||  | |||||||   ||  ||    ||  || | |||||   || ||| || |  |    ||||     |  | |   |  ||   ||||  | ||| ||||| || ||||| |||||||| ||||||||||| ||||| || || ||| ||||||| || ||||| ||||| ||||
gttaggattttttattttttatttttaatgcaaattcttagcagtatatattcttgattccacttgcagcacatttcagcagcttttggtatttggtgcattttgcagGTCGTGGTGCCAAGGAGGCAAATCTGTACACTGAAATAGCTGAAGGCATTCATTCTTATGGTATTACAAGGCATCGCCATG

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|74234670|gb|DT642584.1|DT642584
EST:     CAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATC
genomic: CAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGT-GGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATC
EST: gi|87155331|gb|DY400120.1|DY400120
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
EST: gi|26558690|gb|CA830925.1|CA830925
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAG-GGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
EST: gi|67010559|gb|CO439308.1|CO439308
EST:     CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAG                         GACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC
genomic: CAAGCTAACCAACATTATTATTGATGCAAAATCTGGAGTCAGTGGTGCAGgttcgtattt ... atcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatatctgtttcaacatcaaatgatttggtctctaaaacatgcatcattgtagGACGTGGGGCTAAGGAAGCAAATCTTTACACTGAAATCGCTGAGGGTATCCATGCTTATGGGATAACAAGCCATCGGCATG
                                ctctaaa  putative branch site (score: 3)
                    aaatgattt  TA-rich tract