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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaatgcatgagaattgttgttctattatgttcttcccacagtttttgttttctgcacgttgtggaattcactaactgttgtaatgttgtctttgtagCTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGACCAATAAACTTTGTGATAAGTTGATAAATGGAAAGGACCAGCATCGGGAT

Basic information

species Zea mays
transcript GRMZM2G168629_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 3
tttcaatgcatgagaattg-ttgttctattatgttcttcccacagtttttgttttctgcacgttgtggaattc---actaa-ctgttgtaatgttgtctttg--tagCTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGACCAATAAACTTTGTGATAAGTTGATAAATGGAAAGGACCAGCATCGGGAT
   ||||   ||| |     ||||||| ||||||| | | ||   ||   || |||||||| |  |||  | |     ||| ||||  || |  |    |||  ||||||||| ||||| |||||||||||||||||||| ||||| |||||||||||||| |  ||||||||||||||  | |||||||||||||| ||||| || 
--gcaatt--tgatacccaattgttctgttatgttttccaca---ttccggtgttctgcacttcatggtttgctatgttaatctgtattattacttctcttggttagCTTGGCTCCACTTGTCAAGAAGGTTGGTGAGGATAGGGTGGTGGAGATGACCAACATTCTTTGTGATAAGTTACTCAATGGAAAGGACCAACATCGAGAC

upper sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 3
tttcaatgcatgagaattg-ttgttctattatgttcttcccacagtttttgttttctgcacgttgtggaattc---actaa-ctgttgtaatgttgtctttg--tagCTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGACCAATAAACTTTGTGATAAGTTGATAAATGGAAAGGACCAGCATCGGGAT
   ||||   ||| |     ||||||| ||||||| | | ||   ||  ||| |||||||| |  |||  | |     ||| ||||  || |  |    |||  ||||||||| ||||| |||||||||||||||||||| || || |||||||||||||| |  ||||||||||||||  | |||||||||||||| ||||| || 
--gcaatt--tgatacccaattgttctgttatgttttccaca---ttcctgtgttctgcacttcatggtttgctatgttaatctgtattattacttctcttggttagCTTGGCTCCACTTGTCAAGAAGGTTGGTGAGGATAGTGTGGTGGAGATGACCAACATTCTTTGTGATAAGTTACTCAATGGAAAGGACCAACATCGAGAC

upper sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 2
tttcaatgcatgagaattgttgttctattatgttcttcccacagtttttgttttctgcacgttgtggaattcactaactgttgtaatgttgtct----ttgtagCTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGACCAATAAACTTTGTGATAAGTTGATAAATGGAAAGGACCAGCATCGGGAT
    | |||||     |||   |   |  |||   |  |  ||   |      |  |     | |  | ||   || | |||  ||| |  |      ||| ||  | || ||  | || | ||||||  ||||||  ||||||||||| ||||||| |||||| ||||| || ||| ||||||| ||||| |||||||| || 
---tagtgcattcaggttgccatgagaaaatgaagtaac-gcatgataaaacattagtgttgttttaatttatttatcagttcaaatttgattaaaaattgcagTCTTGCTCCGTTAGTGAGGAAGGTGAGTGAGGTAAGGGTTGTGGAAATGACCAGTAAACTATGTGACAAATTGCTAAATGGGAAGGATCAGCATCGTGAC

upper sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 3
tttcaatgcatgagaattgttgttctattatgttcttcccacagtttttgttttctgcacgttgtggaattcactaactgttgtaatgttgtct----ttgtagCTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGACCAATAAACTTTGTGATAAGTTGATAAATGGAAAGGACCAGCATCGGGAT
    | |||||     ||| ||    |  |||   |  | |||   |      |  |     | |  | ||   || | |||  ||| |  |      ||| ||  | || ||  | || | ||||||  ||||||  ||||||||||| ||||||| |||||| ||||| || ||| ||||||| ||||| |||||||| || 
---tagtgcattcaggttgctgcaagaagatgaagtaac-acatgataaagcattagtgttgttttaatttatttatcagttcaaatttgattaaaaattgcagTCTTGCTCCGTTAGTGAGGAAGGTGAGTGAGGTAAGGGTTGTGGAAATGACCAGTAAACTATGTGACAAATTGCTAAATGGGAAGGATCAGCATCGCGAC

upper sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 4
tttcaatgcatgagaattgttgttctattatgttcttcccacagtttttgttttctgcacgttgtggaattcac--taactgttgtaatgttgtctttgtagCTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGACCAATAAACTTTGTGATAAGTTGATAAATGGAAAGGACCAGCATCGGGAT
 ||    ||||||    | |||   |   |  | |        |      |    |||   || || ||||| |  |   |||| |||| | | | ||| ||  | || ||  | |||||||||||  |||||    |  | ||||||||||||||||||||||| ||||| ||| ||||||| || || || ||||| || 
-ttttgggcatgaatgcttttggatttgaacatacaagtagttgaacagttacattgctttttatgtaattctcgttccttgttttaatat-ggcattgcagTCTTGCACCTTTGGTCAAGAAGGTCAGTGAGACACGACTAGTGGAGATGACCAATAAACTTTGCGATAAATTGCTAAATGGGAAAGATCAACATCGTGAC

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|32934057|gb|CF038869.1|CF038869
EST:     CAACAGCTTGAGGATGCTTCGGGAGATGTTTCTGGTTTAGCTGTTAAATG                         CTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGAC
genomic: CAACAACTTGAGGATGCTTCGGGAGATGTTTCTGGTTTAGCTGTTAAATGgtatgcttca ... gtctttgtagCTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttttctgcacgttgtggaattcactaactgttgtaatgttgtctttgtagCTTGGCCCCACTCGTCAAGAAGGTTGGTGAGGACAGGGTTGTGGAGATGACCAATAAACTTTGTGATAAGTTGATAAATGGAAAGGACCAGCATCGGGAT
                          cactaac  putative branch site (score: 1)
                                           ttgtcttt  putative PPT
                                   ttgtaat  TA-rich tract