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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttatatttattttagttgaaaattgggacatgaagattataataaaccccttaaagtgtgtatatataccatcatcttttgcaattttaatcatgcagGGATGCTGAAACTATTAACGACGCAGTTGAATTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTTCGGATGCAACATCTG

Basic information

species Zea mays
transcript GRMZM5G825524_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825524_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 4
agttatatttattttagttgaaaattgggacatgaagattataataaaccccttaa-agtgtgtatatataccatcat------cttttgcaattttaatcatgcagGGATGCTGAAACTATTAACGACGCAGTTGAATTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTTCGGATGCAACATCTG
       ||| |  |    | | || |  || | |   ||||  |   | | || | |||   ||  | |  | | ||      ||||||||| ||| ||||  |||||||||||| |  ||||||| ||||||||| ||||||||||||||||||||||||||||||||||||||||| || |||||||||| |
------ttttgtcctgaaagtatat-gctacttcacatttatgttcttctcttttacagtacctaattgtttctttatacctgccttttgcaactttcatcacacagGGATGCTGACAGCATTAACGTCGCAGTTGAGTTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTCCGAATGCAACATCAG

upper sequence: GRMZM5G825524_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G40270.1 (Glycine max), 3'ss of exon 4
agttatatttattttagttga--aaattgggacatgaagattataataaaccccttaaagtgtgtatatataccatcatcttttgcaattttaatcatgcagGGATGCTGAAACTATTAACGACGCAGTTGAATTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTTCGGATGCAACATCTG------
    || || | ||| |   |  | |||  |  || | | ||  | |         |   |      |      ||       |||   | |  || ||||||||  || | | | | |  |||||||||||||||||||| |||||||||| ||||||||| || || ||||||||| ||||    | |      
--caattttcaatttggaaaattatattttggtattatgtttggactgggtgtacaagcattaaaggaatggagattgaaaggtgcctctgttgtcctgcagGGAATCTAATAGTGTGATGGACGCAGTTGAATTTGTTCTACAGAATTTCACAGAAATGAATAAGCTTTGGGTTCGGTTGCAGTTGCAGCATCAG

upper sequence: GRMZM5G825524_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G37870.1 (Glycine max), 3'ss of exon 5
agttatatttattttagttga--aaattgggacatgaagattataataaaccccttaaagtgtgtatatataccatcatcttttgcaattttaatcatgcagGGATGCTGAAACTATTAACGACGCAGTTGAATTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTTCGGATGCAACATCTG------
    || || | ||| |   |  | |||     || | | ||    |         | | |    |||      ||       |||   | |  || | ||||||  || | | | | |  || ||||| ||||||||||| |||||||||| ||||||||| || || ||||||||| ||||    | |      
--caattttcaatttggaaaattatatttttgtattatgtttggtctgggtggacaagaattaaaataatggagattgaaaggtgcctctgttgtccttcagGGAATCTAATAGTGTGATGGATGCAGTAGAATTTGTTCTACAGAATTTCACAGAAATGAATAAGCTTTGGGTTCGGTTGCAGTTGCAGCATCAG

upper sequence: GRMZM5G825524_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ27365 (Selaginella moellendorffii), 3'ss of exon 4
agttatatttattttagttgaaaattgggacatgaagattataataaaccccttaaagtgtgtatatataccatcatcttttgcaattttaatc--atgcagGGATGCTGAAACTATTAACGACGCAGTTGAATTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTTCGGATGCAACATCTG
                                                         || ||| | ||      |   |  |    |   ||    ||||||||| |  |  | | | || || || || || ||||| |||||||||||||  |||||||| || |||||||| ||||||||||| | |
---------------------------------------------------------gtatgtttttaagtttgccgttgctaagctcacaacgcaatgcagGGAAGGAGGTAGTGTCAATGATGCCGTGGAGTTTGTGCTTCAGAATTTCACGGAAATGAATAAGCTCTGGGTCCGGATGCAACACCAG

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|19351762|gb|BM896294.1|BM896294
EST:     TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGG                         GGATGCTGAAACTATTAACGACGC
genomic: TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTAACGACGC
EST: gi|22491272|gb|BU051195.1|BU051195
EST:     TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGG                         GGATGCTGAAACTATTAACGACGC
genomic: TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTAACGACGC
EST: gi|18964924|gb|BM661289.1|BM661289
EST:     TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGG                         GGATGCTGAAACTATTAACGACGC
genomic: TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTAACGACGC
EST: gi|32824252|gb|CD963974.1|CD963974
EST:     TCTCAAATAAGCAGAGACAAATCGCCTGATATTGGTTCCGAGTATGAAGG                         GGATGCTGAAACTATTA
genomic: TCTCAAATAAGCAGAGACAAGTTGCCTGATATTGGTTCCGAGTATGAAGGgtactgtacc ... aatcatgcagGGATGCTGAAACTATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccccttaaagtgtgtatatataccatcatcttttgcaattttaatcatgcagGGATGCTGAAACTATTAACGACGCAGTTGAATTTGTTCTTCAGAATTTCATAGAAATGAACAAACTCTGGGTTCGGATGCAACATCTG
                                         ttttaat  putative branch site (score: 3)
                                 ttttgcaattttaat  TA-rich tract