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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtgactaaaataattttttgatgttgttgttgatgatgatactatgtgagcactattgttatatttctaatcattttctgttttggcaactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA

Basic information

species Zea mays
transcript GRMZM5G862101_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862101_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 3'ss of exon 2
cttgtgactaaaataattttttgatgttgt-tgttgatgatgatactatgtgagcactattgttat-atttctaatcattttctgttttggcaactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA
   || | ||  ||  | || | ||    | | |||    |   | | | |||  | |  |||||| || | ||   || ||   |||| |||  | ||||||||||| ||||| ||||||||||| ||||||  |||||| ||||||||||| |||||||||||||||||| ||||||| ||| |||||||||||||||| 
---gtaagtattattttgttgtaattcaatattttgccattttgattgtttgattatttctgttattatatatatatatatttacttttcgcacttctgcagATATGCCTCTGTGAGAGCAATAGAAACAAAATCTCCTGTTGATGATCAGCAATGGCTCACTTACTGGGTGCTGTACTCGTTTATCACTTTGTTTGAGCTT

upper sequence: GRMZM5G862101_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G10730.1 (Glycine max), 3'ss of exon 2
------------------------------------------------cttgt-gactaaaataatttt-ttgatgttgttgttgatgatgatactatgtgagcactattgttatatttctaatcattttctgttttggcaactt--tgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA
                                                 |||| || |     |  |   || ||    ||||       ||    |  | |     | || | ||||| | ||   | |  ||||| |     |  ||||||||||||||  |||| || || ||||  ||   |||  | |||||||||||||||||||||||||||||  | ||||| ||  ||||  | ||||| || 
gtaagtgcaatcttaatcttcctcgtttccttacatacactatgtgtttttgttgaatgttccatctgcatttattccattgtcctgtgagaggtcaaattattgtgactgatttattttttattgatgtgggttttcgtgttgtgctgcagATATGCTTCAATTAGGGCGATTGAGAGCAAGTCTCCCATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACACTCTTTGAACTT

upper sequence: GRMZM5G862101_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G01160.1 (Glycine max), 3'ss of exon 2
--------------------------cttgtgactaaaataattttttgatgttgttgttgatgatgatactatgtgagcactattgttatatttctaatcattttctgttttggcaactt--tgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA
                           |  | ||    | ||| | ||    |   ||||  |  ||    |||   |    |    | ||   | | ||   | |  ||||| |    ||  | ||||||||||||  |||| ||||| ||||  ||   |||| | |||||||||||||||||||||||||||||  | ||||| ||  ||||  | ||||| || 
gtaagcaaaatcttgatcttcctcttttccttacacgcacaatgtgttttgttgaatgttccttttgcatttattccattgttggactcattcatattattgatgtgggttttcgtgttttgcttcagATATGCTTCAATTAGGGCAATTGAGAGCAAGTCTCCTATTGATGATCAGCAGTGGCTCACTTACTGGGTTCTCTACTCCTTGATCACCCTCTTTGAACTT

upper sequence: GRMZM5G862101_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g05990.t01 (Vitis vinifera), 3'ss of exon 2
cttgtgactaaaataattttttgatgttgttgttgatgatgatactatgtgagcactattgttatatttctaatcattttctgttttggcaactttg-cagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA
| |||   |   ||||| | | | | |   ||||  || |     | | ||||    | |    |    ||  |  |||  ||   |||   ||||| ||||||||| ||  |||| ||||| ||||| ||    ||||| ||||||||||| |||||||| |||||||| ||||| ||  |  ||||  | || ||||| 
catgtatgttctataatatgt-ggtttgaatgtttgtgttttagttttctgagagaaaattgcttgaaacttttgttttggtgggctggtttctttgacagATATGCCTCAATTAGGGCAATTGAGACCAAGTCCCCTGTTGATGATCAGCAATGGCTCACATACTGGGTTTTGTATTCTATGATCACACTCTTCGAGCTC

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|211223200|gb|FL136732.1|FL136732
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|32858463|gb|CD998144.1|CD998144
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCGATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|14245109|gb|BG873691.1|BG873691
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211223194|gb|FL136726.1|FL136726
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|71771977|gb|DR969914.1|DR969914
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211223203|gb|FL136735.1|FL136735
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211223202|gb|FL136734.1|FL136734
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211223197|gb|FL136729.1|FL136729
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211221143|gb|FL136724.1|FL136724
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211223201|gb|FL136733.1|FL136733
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211223204|gb|FL136736.1|FL136736
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
EST: gi|211223195|gb|FL136727.1|FL136727
EST:     GCCACTCATATCACTTGCTTATCCTCT                         ATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA
genomic: GCCACTCATATCACTTGCTTATCCTCTgtaagtatct ... aactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgagcactattgttatatttctaatcattttctgttttggcaactttgcagATATGCTTCTGTTAGAGCAATAGAGACAAAAAATCCTGTAGATGATCAGCAGTGGCTCACTTACTGGGTGTTGTACTCATTTGTCACTTTGTTTGAGCTA
                      ttctaat  putative branch site (score: 2)
           tattgttatatttcta  TA-rich tract