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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagtctgcttcgattttgtttcagagcaagaatcattgagcattttcactttcttatttgatagcctgctcttctcattctctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG

Basic information

species Zea mays
transcript GRMZM2G069758_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
atagtctgcttcgattttgtttcagagcaagaatcattgagcattttcactttcttatttgata-gcctgctcttctcattct--ctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG------
 |||| |     |  ||||||| |   |||| |          ||||   |||    ||||||| |  || |||  |    ||  ||  ||  |  |||| |||| || |||||||||||||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||      
ttagtgtatgatggatttgtttta---caagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG

upper sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 2
atagtctgcttcgattttgtttcagagcaagaatcattgagcattttcactttcttatttgata-gcctgctcttctcattct--ctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG
 |||| |     |  ||||||| |   |||| |          ||||   |||    ||||||| |  || |||  |    ||  ||  ||  |  |||| |||| || |||||||||||||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||
ttagtgtatgatggatttgtttta---caagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG

upper sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G33970.1 (Glycine max), 3'ss of exon 2
atagtctgcttcgattttgtttcagagcaagaatcattgagcattttcactttcttatttgatagcctgctcttctcattct--ctgattgctccaattc--agGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG
 | | |   |   | |    || |  |  |   |  |        | ||  ||  ||  | ||    | | |||  |||| |  ||| |||||   ||||  ||||||||||||| || ||||| || ||||| || |||||  | || || | ||||||||||||||| || ||||| |||||||| ||||||||||
ctcggcaattggcaataccctttaatgtca---ttgtcagttgcatgcagcttgctaactaattaattac-cttgacattgtggctgtttgctattattctcagGGGTATGTTGGTAATAAATCCGCTGTCTTCCCTCTGCAATTACTGGGATATGATGTGGATCCAATTAATTCTGTGCAGTTTTCGAATCATACAG

upper sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G04360.1 (Glycine max), 3'ss of exon 2
atagtctgcttcgattttgtttcagagcaaga----atcattgagcattttcactttcttatttgatagcctgctcttctcattctctgattgctccaattc--agGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG-
    | |  |   | ||||    |      ||    || ||  |     | ||  ||  ||| | ||  |||   |||        ||| |||||   ||||  ||||||||||||| || ||||| || ||||| || ||||| || || || | |||||| |||||||| || || || |||||||| |||||||||| 
----tttcttggcaatttgcagtaatctttgatgttattatcaattgcatgcagcttgctatgtaattaccttgactttgtg---gctgtttgctattattctcaggGGTATGTTGGTAATAAATCCGCTGTCTTCCCTCTGCAACTACTGGGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG

upper sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G37850.3 (Arabidopsis thaliana), 3'ss of exon 2
atagtctgcttcgattttgtttcagagcaagaatcattgagcattttcactttcttatttgatagcctgct--cttctcattctctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG
 |      ||  | ||  |||    | |     |  ||  |  | |     |   |       |   || |  | | | ||      ||| ||     | |||| |||||||| |||||||| || |||||||| || ||  |  | || | ||||||||||||||| ||||||||||| || || ||||||||||
ctgtctctctatgcttgagttctgcaacttttttttttttgtgtgtgtgtgtgtgttaccagaaatgtgatgccattttatatgtctattacttt--cttagGGATATGTTGGTAACAAATCAGCTGTCTTTCCTCTTCAATTGTTGGGGTATGATGTGGATCCAATCAACTCTGTACAATTCTCGAATCATACAG

upper sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
atagtctgcttcgattttgtttcagagcaagaatcattga-gcattttcactttcttatttgatagcctgctcttctcattctctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG
| |  |   ||| |  |    | |  | |   |   || | |  |||    |   |||| |    | ||   ||||     |  |   |  | |   | |||| ||||||||||| |||||||| ||||||||||| ||||| || |||| |||||| |||||||| || || |||||||| || ||||| ||||
aaacaccatttcaacataagcttat-gtagttacatttaatgtgtttgtggtagattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG

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|211131902|gb|FL371916.1|FL371916
EST:     TGCCGTCTGACACCGGCCGTGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTT
genomic: TGCCGTCTGACACCGGCCGTGTGCTCAGCATCCAGTCCCACACCGTCCAGgttcagcccg ... tccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTT
EST: gi|211278750|gb|FL388232.1|FL388232
EST:     TGCCGTCTGACACCGGCCGTGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTT
genomic: TGCCGTCTGACACCGGCCGTGTGCTCAGCATCCAGTCCCACACCGTCCAGgttcagcccg ... tccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcactttcttatttgatagcctgctcttctcattctctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG
                                   ctctgat  putative branch site (score: 4)
                                         ttgctcc  CT-rich tract
     tttcttatttgata  TA-rich tract