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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgagaactggatactttttgagatagatcatttactgaatgcctcgcttgactcaatttttagtaactggactaggttatactttaaaaaactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAA

Basic information

species Zea mays
transcript GRMZM2G020002_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 9
ctgagaactggatactttttgagatagatcatttactgaatgcctcgcttgac-tcaatttttagtaactggactaggttatactttaaa---aaactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAA
    | | ||   |       |||||  |   ||  |  |    | ||  ||  ||    |||   ||    |  |  |  |  |  |||   | |||||||||||||||||||||| |||||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||||| ||| ||||||||
---tggattgatcatgcccc-agatatctacattgatataaatttggcaagatatctcaatttgacaaacaaagcatatattgatacaaattcatactttgcagGGCAGAGAGTCATTGGTGAACCTGTGGTTTCTGGGCTAGTACTTGATGATTCTTGGCTTTGGGATCCGGACTTCATGATAGCTTCAAA

upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------------ctgagaactggatactttttga---gatagatcatttactgaat-gcctcgcttgactcaatttttagtaactggactaggttatac----------tttaaaaaactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAA
                                                                            ||   | | | | |     |      |||    || |   |||  |   |  |  | |   |  ||||||  |||  ||    |||           |||   |    || |||| ||||  || || || || ||||| || |||||| || | |||||||||  |||||||||||||||||||||||| ||||| || ||
gttttctgttacaactcatgtaggactaaccttttgcttttctcattgtatggacattatcctgttagaaatcaatctcctatccgaacatccactagtgcaataacatatgtgtagaaaagtacctttcaaatttttacttagtatttggcttaataaatatgaaaagtttttttgttatgtatttcagGACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGATGATCATTGGCTTTGGGATCCTGACTTCACAATTGCGTCCAA

upper sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
---ctgagaactggat--actttttgagatagatcatttactgaatgcctcgctt---gactcaatttttagtaactggactaggttatactttaaaaaactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAA
    ||| | ||| |   |  || |||   | |  |||  ||||     |   ||   | || |||    ||||||   | |   || |  ||| ||      |||||| ||||| || || || || || || ||||||||  |||| |||||||||||| |||| ||||||||||||||||  |  ||  ||||
taggtgatatctgaactgaacttctgatgca-actattatctgatctaatgattttgagtcttaatcaggagtaacc--attcacttttcttttgaa-----ctgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA

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|18659090|gb|BM500149.1|BM500149
EST:     TGTGATGAGCATCGACGCAATGGATGAGATTGCCAAGGCTAAAAGAGAAG                         GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATT
genomic: TGTGATGAGCATCGACGCAATGGATGAGATTGCCAAGGCTAAAAGAGAAGgtcagcttgg ... aactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATT
EST: gi|31355355|gb|CD439712.1|CD439712
EST:     TGTGATGAGCATCGACGCAATGGATGAGATTGCCAAGGCTAAAAGAGAAG                         GGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATT
genomic: TGTGATGAGCATCGACGCAATGGATGAGATTGCCAAGGCTAAAAGAGAAGgtcagcttgg ... aactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcttgactcaatttttagtaactggactaggttatactttaaaaaactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAA
                tagtaac  putative branch site (score: 1)
                                ttatactttaaaaaac  TA-rich tract