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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcacctttgttgttaattgacagtctgtaggttttttcctcttgatactttgtgagcagtattgttatatttctaaccactttctgttttggcacctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA

Basic information

species Zea mays
transcript GRMZM2G047860_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
gtaagtatcacctttgttgttaattgacagtctgtaggttttttcctcttgatactttgtgagcagtattgttatatttctaaccactttctgttttggcacctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
|||||||| |  |||||||| | |  | | | ||    |||  |  | |   || ||         | || |||||| | ||   | || ||  ||| |||| | ||||||||||| ||||| ||||| ||||| ||||||  |||||| ||||||||||| |||||||||||||||||| |||||||||||||||||||||||||||| 
gtaagtattat-tttgttgtaattcaatattttgccattttgattgtttgattatttc--------tgttattatatatatatatatttact--tttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT

upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G10730.1 (Glycine max), 3'ss of exon 2
------------------------------gtaagtatcacctttgttgttaattgacagtctgtaggttttttcctcttgatactttgtgagc----agtattgtta------tatttctaaccactttctgttttggcacctt--tgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
                               ||  ||     | |||| ||  |  |   ||  |  |  |||    | |  | || || |||     | |||||| |      ||||| | |    | |  ||||| |     |  ||||||||||||||  |||| || || ||||  ||   |||  | |||||||||||||||||||||||||||||  | ||||| || |||||  | ||||| || 
gtaagtgcaatcttaatcttcctcgtttccttacatacactatgtgtttttgttgaatgttccatctgcatttattccattgtcctgtgagaggtcaaattattgtgactgatttattttttattgatgtgggttttcgtgttgtgctgcagATATGCTTCAATTAGGGCGATTGAGAGCAAGTCTCCCATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACACTCTTTGAACTT

upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G01160.1 (Glycine max), 3'ss of exon 2
------------gtaagtatcacctttgttgttaattgacagtctgtag-gttttttcctcttgatactttgtgagcagtattg---ttatatttctaaccactttctgttttggcacctt--tgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
             | |   ||  ||||    |  |   ||| | |||   |||   |  || |  | | ||     || | |||   | ||   | | |    | |  ||||| |    ||  | ||||||||||||  |||| || || ||||  ||   |||| | |||||||||||||||||||||||||||||  | ||||| || |||||  | ||||| || 
gtaagcaaaatcttgatcttcctcttttccttacacgcacaatgtgttttgttgaatgttccttttgcatttattccattgttggactcattcatattattgatgtgggttttcgtgttttgcttcagATATGCTTCAATTAGGGCAATTGAGAGCAAGTCTCCTATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

upper sequence: GRMZM2G047860_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
gtaagtatcacctttgttgt-taattgacagtctgtaggttttttcctcttgatactttgtgagcagtattgttatatttctaaccactttctgttttggcacctttg-cagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
        ||  | |||| | ||||     || || | |||| |   | ||  |  | || ||| |   |  ||  |  | |      ||  ||   |||   ||||| ||||||||| ||  |||| || || ||||| ||    ||||| ||||||||||| |||||||| |||||||| ||||| ||  | |||||  | || ||||| 
--------catgtatgttctataatatgtggtttgaatgtttgt--gttttagttttctgagagaaaattgcttgaaacttttgtt--ttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC

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|211371979|gb|FL186724.1|FL186724
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|32808662|gb|CD960896.1|CD960896
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211371978|gb|FL186723.1|FL186723
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatca ... acctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgagcagtattgttatatttctaaccactttctgttttggcacctttgcagATATGCTTCTGTTAGAGCTATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCGTTTATCACTTTGTTTGAGCTA
                      ttctaac  putative branch site (score: 1)
                                            caccttt  putative PPT
           tattgttatatttcta  TA-rich tract