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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgatctttgtcacctaaatttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA

Basic information

species Zea mays
transcript GRMZM2G124886_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 16
gtgagttgatctttgtcacctaa-atttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
||||||   |  |||||   ||   | |||  |   |       |   || ||||| || |||  |  ||| ||| ||||||||||||||||||||||||||||||| | |||| |||||||||||||||||||||||||| || || ||||||||||| | | ||||| |||||||||||
gtgagtct-tggttgtctggtatcgtatcatattcggaagccacaatgaacttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACTATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 7
gtgagttgatctttgtcacctaaatttcacttgtagtttttgtacacaag----ttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
    ||   |||| ||   ||    ||   |  || | |     |||||     ||||| || |||  |  ||| ||| |||||||||||||||||||||||||||||||   |||| |||||||||||||||||||||||||| || || ||||||||||| | | ||||| |||||||||||
----gtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaacttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
----gtgagtt---gatctttgtcacctaaatttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
    | ||| |   || ||      |   ||| | |||  |  | ||  |  |   | |||     || |    || | |  ||||||||| |||| ||||| ||||| || | |||||| ||||| || ||||||||||||||||| || ||| | ||||||| |||  ||||| | |  || || 
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

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|60337834|gb|DN204807.1|DN204807
EST:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttgat ... tttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
                               ggctaat  putative branch site (score: 3)
                                         cttttttatt  putative PPT
                                  taatgtacttttttat  TA-rich tract