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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggatgtaacattttgtcaacttgctttacatttcacaaatacttgtctaattattttttaaccaatatcatgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAG

Basic information

species Zea mays
transcript GRMZM2G130230_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 6
gtaatggatgtaacattttgtcaac----ttgctttacatttcacaaatacttgtctaattattttttaaccaatatcatgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAG
||||||| | |||  |||||||||     | |  | |  |    | |||||||| |||| || |||| || ||||  ||| ||||||||||| ||||||||||||||||| || |||||||||||||||||||| |||||||||||||||||||||
gtaatggctataa--ttttgtcaagaatgtgggatgatttcctccgaatacttgactaactacttttgaaacaatcgcatttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG

upper sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 6
gtaatggatg-taacattttgtcaacttgctttacatttcacaaatacttg-tctaattattttttaaccaatatcatgtcac-agCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAG
||| |  ||| |  | | ||| |  ||    || | |    || | |||||  |||||   | |  |    |  |  | | || || | || ||||||||||| |||||||||||| ||||||| |||||||| ||||| |||| |||| | |||
gtagtaaatgattgcttattggct-ctcatattgcttgcttcataaacttggcctaatccctctccatttgac-ttgtattaccagTTAGTACTTCGTTTTGCAAACCGATTATTCATGCCTCTATGGAACCGTGACAACATTGCTAATGTGCAG

upper sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G24250.2 (Glycine max), 3'ss of exon 6
gtaatggatg-taacattttgtcaacttgctttacatttcacaaatacttgtctaattatt------ttttaaccaatatcatgtca-cagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAG
|||||  ||| | | |   || |  |||| ||    |||||  |||  ||| ||||| |||      |||  |   |  | || |   ||| | || ||||| ||||| || || || |||||||| ||||||||||||||||| ||||| ||| |||||
gtaataaatgattatacaatggcttcttgttt---gtttcatgaat-tttgcctaatgattaatccctttacatttaacttatattggcagTTGGTACTTCGCTTTGCAAATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAATGTACAG

upper sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 6
gtaatggatgtaacattttgtcaacttgctttacatttcacaaatacttgtctaattatt------ttttaaccaatatcatgtca-cagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAG
|||||  ||| |  ||    |    |   | |   |||||  | |  ||| ||||| |||      |||  |   |  | || |   ||| | || ||||| ||||| || || || |||||||| ||||||||||||||||| ||||| ||  |||||
gtaataaatg-attatacaatggcttctttgtttgtttcatgagt-tttgcctaatgattaatccctttacatttaacttatattggcagTTGGTACTTCGCTTTGCAAATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG

upper sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaatggatgtaacattttgtcaacttgctttacatttca--caaatacttgtctaattattttttaaccaatatcatgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAG
||||   || |    || |    | | | ||   | || |  ||||||    | ||||  |     |  ||   | |     ||| | |||||||| |||||||| || || || ||||| || |||||||||||||||||||  ||  |||||
gtaacacatatttgcttctagtcattagtttattaatttagacaaataaagatataatc-taacgcattcatcgttag--tgcagTTGGTTCTTCGGTTTGCCAATCGCTTGTTTTTGCCACTATGGAACCGCGACAATATTGCAAACGTACAG

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|74237092|gb|DT645006.1|DT645006
EST:     AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTG                         CTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGGACCGCGAC
genomic: AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTGgtaatggatg ... catgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
EST: gi|71449499|gb|DR830549.1|DR830549
EST:     AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTG                         CTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGGACCGCGAC
genomic: AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTGgtaatggatg ... catgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
EST: gi|67037531|gb|CO464345.1|CO464345
EST:     ATCTATACAGAATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTG                         CTTGTTCTTCGTTTTGCCAACCGATTGTTCTTGCCTCTTTGGAACCGCGAC
genomic: A-CTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTGgtaatggatg ... catgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
EST: gi|71447340|gb|DR828390.1|DR828390
EST:     AACTATACAGGATAGACCATTACCTGNGAAAAGAGTTGGTCCAAAACTTG                         CTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
genomic: AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTGgtaatggatg ... catgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
EST: gi|89759526|gb|DY688327.1|DY688327
EST:     AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTG                         CTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
genomic: AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTGgtaatggatg ... catgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
EST: gi|78083439|gb|DV511832.1|DV511832
EST:     AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTG                         CTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
genomic: AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTGgtaatggatg ... catgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
EST: gi|78109778|gb|DV528194.1|DV528194
EST:     AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTG                         CTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
genomic: AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTGgtaatggatg ... catgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGAC
EST: gi|71449885|gb|DR830935.1|DR830935
EST:     AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTG                         CTTGTTCTTCGTTTTGCCAACTGATTATTCTTGCCTCTTTGGGACCGC
genomic: AACTATACAGGATAGACCATTACCTGGGAAAAGAGTTGGTCCAAAACTTGgtaatggatg ... catgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttacatttcacaaatacttgtctaattattttttaaccaatatcatgtcacagCTTGTTCTTCGTTTTGCCAACCGATTATTCTTGCCTCTTTGGAACCGCGACAATATTGATAATATACAG
                                ttttaac  putative branch site (score: 2)
           acaaatacttgtctaa  TA-rich tract