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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcagctagggttactgtagcactgtagctctctctctcactttcaagcacaatggaatctatctataattgtcagctgcaaatgacagttctcatgcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAGAATCTTGGCATTTTGAAAATTCAATTTCCCAGTGTTCCAATGATAGCTT

Basic information

species Zea mays
transcript GRMZM2G451856_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 5
----ctcagctagggttactgtagcactgtagctctctctctcactttcaagcacaatggaatctatctataattgtcagctgcaaatgacagttctcatgcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAGAATCTTGGCATTTTGAAAATTCAATTTCCCAGTGTTCCAATGATAGCTT
    |  ||||||  ||    ||    |  |||  |    | ||  |  |   | | |     | ||    ||||      || || | |  ||| ||||||||||||| ||||||||||| |||||||| ||||||||||| || ||||||||||||||||||||||| ||  | || |||||||||||||| ||||||||||
tgagcatagctag--ttgacatatgttttaagcagttaagcacatgtgtatctagagtctg--cgattaccaatttatcattgtaattaagtgttatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAGAATCTTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTT

upper sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 4
ctcagctagggttactgtagcactgtagctctctctctcactttcaagcacaatggaatctatctataattgt-cagctgcaaatgacagttctcat-gcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAGAATCTTGGCATTTTGAAAATTCAATTTCCCAGTGTTCCAATGATAGCTT
   |   |   || |       ||  | |  ||||      |   |   |   ||   |   | ||| |   |  |  | |   | |  |||  ||| |||||| || || |||||||| |||||||||||||| ||||| |||||||||||||  ||  | ||| | || |  || || ||  ||||||| ||  | ||||
--gactcactatttcctctatccttcaacagtctcagagtttcatagcaatgctgtgttagttgtatgacaatataattcctggttatggtttgcattgcagGAAGCACATTGCTGTAGTCAATGGGGTCATGACTTTCGACCTGACTACAAGAGCCTCAGTATTCTCAAGACACAGTTCCCTCGTGTTCCTATTGTTGCTT

upper sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------------------------ctcagctagggttactgtagcactgtagctct--ctctctcactttcaagcacaatg---------gaatcta-tctataattg-tcagctgcaaatgac-agttctcatgcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAGAATCTTGGCATTTTGAAAATTCAATTTCCCAGTGTTCCAATGATAGCTT
                                         ||| || |    |  | |  | || | ||| |   |   |    |  |  | ||  |          || ||| | ||| | || |||  | |  |||    |||    ||||||||||||| || ||||| || ||||||||||||||||| ||||| ||||||||  |  ||||| ||||||  || |||||||  ||||| ||| | ||||
gtaagtctctcctagttttagtttcttactcggaaattgtgctctgccacctatcttctcactctctggctttagtttatttggatatatccgcaccgttaaacagaaaacctactttatgaatgatcaatttcctatgtttggtttctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT

upper sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 4
---ctcagctagggttactgtagcactgtagctctctctctcactttcaagcacaatggaatctatctataattgtcagctgcaaatgac--agttctcatgcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAGAATCTTGGCATTTTGAAAATTCAATTTCCCAGTGTTCCAATGATAGCTT
    |    || | |  ||||   ||  | | | | | | |      ||   | |   ||| ||    |  | |||    ||  |||       ||    | |||||||| || |||||||| || ||||| ||||| ||||| || || ||||| ||||||||||| || || | ||| |||||   ||||||| |  | ||||
ctttttcattatgttatctgtt-taccatggttttattttttgg--gcatttatatatgaagctgc--aggactgtgtaatgttaattctttgattgctttacagGAGGCACATTGCTGTAGTCAGTGGGGCCATGACTTTCGCCCAGATTACAAAAATCTTGGCATCTTAAAGACTCAGTTTCCTGATGTTCCAGTAGTTGCTT

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|60348558|gb|DN215531.1|DN215531
EST:     AGCTCGAGAAATGCCATCATGCCGGTCGTCTTTCTCTGATTGCAATAGAT                         GAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAG
genomic: AGCTCGAGAAATGCCATCATGCCGGTCGTCTTTCTCTGATTGCAATAGATgttagtaatt ... tctcatgcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagcacaatggaatctatctataattgtcagctgcaaatgacagttctcatgcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAGAATCTTGGCATTTTGAAAATTCAATTTCCCAGTGTTCCAATGATAGCTT
                                            ttctcat  CT-rich tract
           aatctatctataatt  TA-rich tract