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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaaagaaccaatgtccacagaaagatgatgtgttattgcttcgtttccattttcagaacccatttgctgtactaattttggtacttctcaatttgcagTGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTTGTGCGAATGTCATCACACTCCTTCAG

Basic information

species Zea mays
transcript GRMZM2G133226_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 1
accaaagaaccaatgtccacagaaagatgatgtgttattgcttcgtttccatttt-cagaaccca---tttgctgtactaattttggta-cttctcaatttgcagTGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTTGTGCGAATGTCATCACACTCCTTCAG
        ||  | |  ||        |  |   || |   || |||| |||||| |||| | ||    |   | |||||| ||||| | ||| |||||  |||||||||||||||||||||||||||||||| || ||||| ||||||||||| ||||| |||||||| || |||||||||
-----ttcacatacggacatcttgttttcgttctttctacatttgttttcatttttcagatctcaggtatcattttactaactttggcaacttttcaatccgcagTGTTGCTAGTGATGTTTAACAAAGCAGCACTGTCTTCATATAATTTCCCCTGTGCAAATGTCATTACGCTCCTTCAG

upper sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0008g05570.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------------accaaagaaccaat--gtccacagaaagatgatg-----tgttattgcttcg---tttccattttcagaacccatttgc-tgtactaattttggtacttctcaattt--gcagTGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTTGTGCGAATGTCATCACACTCCTTCAG
                                        |     ||  |  |   |   |  ||  || ||        |||||  ||     ||| ||||    || ||  ||| | || |||  | |  | | ||||   |||  |||||  |  | ||||| || ||||||||||| || ||||| ||| ||||||||||||| | ||||||||||||| |||||
gtgccctctcttctctaaattgcatcttaatttcatgtgaattctggagtcgtttcatttgcgtaattataataattatcattattattttaattttttcattaatcgatccattttacgtgaactcctctatgcaattctttgtttttgcagTTCTATTGGTGATCTTCAACAAAGCAGCCCTTTCTTCTTATCATTTCCCTTGTGCAAGTGTCATCACACTCTTTCAG
















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|148947034|gb|EC892331.2|EC892331
EST:     CATGACCCGCCGCGGCGGCACCGCCGCGCTCTCTTACATGGCATGCTCCG                         TGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTT
genomic: CATGACCCGCCGCGGCGGCACCGCCGCGCTCTCTTACATGGCATGCTCCGgtacgcgcgg ... caatttgcagTGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTT
EST: gi|91054599|gb|EB165017.1|EB165017
EST:     CATGACCCGCCGCGGCGGCACCGCCGCGCTCTCTTACATGGCATGCTCCG                         TGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTT
genomic: CATGACCCGCCGCGGCGGCACCGCCGCGCTCTCTTACATGGCATGCTCCGgtacgcgcgg ... caatttgcagTGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccattttcagaacccatttgctgtactaattttggtacttctcaatttgcagTGTTGCTAGTGATGTTTAACAAAGCAGCTCTCTCTTCGTATAATTTCCCTTGTGCGAATGTCATCACACTCCTTCAG
                          tactaat  putative branch site (score: 1)
                                      tacttctc  putative PPT
                          tactaatttt  TA-rich tract