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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactaaaatttagttagggtcctaccattttgtgaagaagcatttggatcacgatccattactacccctaacaataactggtttgctaactattttgcagTCGTTGATGATTGCAGCAATTCCAAACGTCATTGGTTGGCTTGCGATCTCCTTTGCAAAA

Basic information

species Zea mays
transcript GRMZM2G160460_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 2
aactaaaattta-gttagggtcctaccattttgtgaagaagcatttggatcacgatccattactacccctaacaataactggtttgctaact--attttgcagTCGTTGATGATTGCAGCAATTCCAAACGTCATTGGTTGGCTTGCGATCTCCTTTGCAAAA
 | |  | || | ||   | |  |  |||  |   |  |  || ||| |   | ||    ||||      | |  ||||||  ||| |   |  ||||| ||||| ||||||||||| |||||||||||| |||||||||||||||| |||||||||||||||
-attttatttaatgtcctgtttttggcatggttgcagtagtcagttgtacttcaatggtctactcttttaagc--taactgaattgtttggtgaattttccagTCATTGATGATTGCTGCAATTCCAAACATCATTGGTTGGCTTGCCATCTCCTTTGCAAAA

upper sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 3'ss of exon 2
aactaaaatttagttagggtcctaccattttgtga--aga--agcatttggatcacgatccattactacc-cctaacaataactggtttgctaact-attttgcagTCGTTGATGATTGCAGCAATTCCAAACGTCATTGGTTGGCTTGCGATCTCCTTTGCAAAA
        ||| |||        |  ||    | |  |||  || | ||  |  ||  |  |   |||     | ||  |||  |  ||||| | | | | | ||||||||||| ||||| ||  |||| ||| |||||||||||||||| |||||||||||||||
-----ttctttggttcatacttcataatcacttaatcagatcagtagtta-actacagtgaagctctattattttactctaatggtcttgctgattgaatctccagTCGTTGATAATTGCGGCGGTTCCTAACATCATTGGTTGGCTTGCCATCTCCTTTGCAAAA

upper sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G36950.1 (Glycine max), 3'ss of exon 3
------------aactaaaatttagttagggtcctaccattttgtgaa--gaagcatttggatc-acgatccattactacccctaacaataactggtttgctaactatt--------ttgcagTCGTTGATGATTGCAGCAATTCCAAACGTCATTGGTTGGCTTGCGATCTCCTTTGCAAAA
               |    |||   || |    | |  ||   | ||  | |  |||||  |    |       |||| | | ||   | |  || || | |  | ||        |||||||| |||||||||||| | ||||| ||  | ||||||||||| || ||||| |||||||| 
ggtaccccttttttttctcttttttctatgtgtatgcttttcctttaactgcaatatttgagtttgagggatgagactaactc-aatggtcaacgggttacaatttcttgtctgaaattgcaGTCTTTGATGATTGCATCCATTCCTAATATTATTGGTTGGCTGGCTATCTCATTTGCAAA-

upper sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G08070.1 (Glycine max), 3'ss of exon 3
---------------aactaaaatttagttagggtcctaccattttgtgaaga--agcatttggatc-acgatccattactacccctaacaataactggtttgctaactatt--------ttgcagTCGTTGATGATTGCAGCAATTCCAAACGTCATTGGTTGGCTTGCGATCTCCTTTGCAAAA
                  |    | |  ||| |    | |  ||   | ||    |  |||||  |    |        |||   | |    | |  || || | |  | ||        |||||||| |||||||||||| | ||||||||  | ||||||||||| || ||||| |||||||||
gtacccttttttctcttttttcgtgtgtttatgtgtatgcttttcctttaatttcaatatttgagtttgagggatgaggctaattcaattggtcaacgggttacaatttcttgtctgaaattgcagTCTTTGATGATTGCATCCATTCCAAATATTATTGGTTGGCTGGCTATCTCATTTGCAAAA

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|211032760|gb|FL421272.1|FL421272
EST:     TCGGGGCGATCGCCAGTGGCCAGATGGCCGAGTACGTTGGCCGCAAAGGG                         TCGTTGATGATTGCAG
genomic: TCGGGGCGATCGCCAGCGGCCAGATGGCCGAGTACGTTGGCCGCAAAGGGgtgagaaact ... tattttgcagTCGTTGATGATTGCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcacgatccattactacccctaacaataactggtttgctaactattttgcagTCGTTGATGATTGCAGCAATTCCAAACGTCATTGGTTGGCTTGCGATCTCCTTTGCAAAA
                                      tgctaac  putative branch site (score: 1)
                                            ctatttt  CT-rich tract
                                         taactatttt  TA-rich tract