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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG

Basic information

species Zea mays
transcript GRMZM2G140689_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 2
--------------------gtgagtgttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
                    | ||    | |||||    |    |  | ||  || | | | |||||||  | | ||  | ||  | | | ||||  ||||| ||||| || |||||| ||||||||||||||||||||||  | |||||||| || ||||| ||||||||||| ||||||||||||||||| || |||
gtgagtgcctaccgcgttttgggatccatttgtttaaagtgtttaacgattattgggat-gattggattaatcaagtcttgttggtttattattt-tagGCCTCAGGTCTCTTCGGCGCTGTTCTTCAGCTACAACACAGCGCTCGGGCCGCCATACCGGGTTATTGTGGATACAAACTTCATCAATTTCTCCATCCAG

upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 3
------------------------gtgagtgttg--tgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgtt--gttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
                             |  |   ||  || | |        || ||  |  || ||| | || || || ||  ||||   | |||  | | ||| ||      ||| || ||| | |||||    |||||||| ||| |||| || || ||||| ||  | ||||| ||||||||||||||||||||||| || 
gtaagcttccatcctcactctttccccccttctaattgactgagtttattgcttttcccccttgttcttttggtt-ttaatctttggtttggatttgtattattcagTCCAACTCATTCTTCAGCGCTTTTCTTTCAATACAACACTGCACTGGGACCCCCTTATCGTGTTTTGGTGGACACCAACTTCATCAATTTCTCGATCCAA

upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtgagtgttgtgtttgcgctcggaat-----ggtttcctgtgcttgtttggattgttga--tgttgttttcttctgtgatt-tacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
               | |    | | |  ||      |||       ||| ||||| ||  |   |||||| |  | || |||  || | |||   | ||||||  | ||| |||| ||  | |||||||  |||||||| || ||||||||||| ||||||||  | ||||||||||| ||||||||||| || || |||
gtaagtttttcttaataaacaatttttccgctgcattaatttcagaatttgctgtgtttaatc--attgttaaattattatttaattttctgaggatgcagGCCATATGTTCCGTCCGCTCTTTTCTTCAAGTACAACACTGCTTTGGGGCCGCCTTATCGGGTTTTGGTGGATACCAATTTCATCAATTTTTCTATTCAG

upper sequence: GRMZM2G140689_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDP01317 (Chlamydomonas reinhardtii), 3'ss of exon 2
-----------------------------------------------------------gtgagt-gttgtgtttgcgctcggaatggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG------
                                                           || | | |||| |  ||| |||  |     | |   | |    |||     |   ||||| |  |  |   |   | |||   | |||| ||||||||| |||||||| ||||||||||     ||||||||||||||| |||| | ||||| |||||||| ||||| ||||| ||  ||      
gtgtgagtgcagcagcggcgctctgccctagcacgctggccacagccaaaaccctgagcgtcaatcgttgggcatgctctcacacatcatgctgctcccgacttgtcacctccctgttgctgcccacgtggtgctgcagtgagaagGTGTCGTCGGCGCTGTTCTTCCGCTACAACACGCAGCTGGGGCCGCCGTATCAGGTGCTGGTGGACACCAACTTTATCAACTTCTCCATCAAGAACAAG

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|31352269|gb|CD436626.1|CD436626
EST:     CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|71445647|gb|DR826697.1|DR826697
EST:     CGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|88754303|gb|DY538444.1|DY538444
EST:     AACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCG-TGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: AACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|88746998|gb|DY531139.1|DY531139
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|74245266|gb|DT653180.1|DT653180
EST:     GGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: GGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|74239821|gb|DT647735.1|DT647735
EST:     GAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: GAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|213173441|gb|FM193835.1|FM193835
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|78025632|gb|DV494019.1|DV494019
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|33468200|gb|CF245249.1|CF245249
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|78077064|gb|DV505498.1|DV505498
EST:     CTGAACCACAAGAAGAAGGACGTGGACAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CTGAACCACAAGAAGAAGGACGCGGACAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
EST: gi|76292363|gb|DV031931.1|DV031931
EST:     CAAGGAGAAACTCGGCCGGAATGT                         GCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC
genomic: CAAGGAGAAACTCGGCCGGAATGTgtgagtgttg ... tgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtttcctgtgcttgtttggattgttgatgttgttttcttctgtgatttacagGCCGCAGGTTTCGTCGGCGTTGTTCTTCAGCTACAACACAGCATTGGGGCCGCCGTATCGGGTGATTGTGGATACCAACTTCATCAATTTCTCGATACAG
                        tgttgat  putative branch site (score: 4)
                                ttgttttcttctgt  CT-rich tract
                                ttgtttt  TA-rich tract