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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgacacacttgtttacataatttattatttttcattatactgaatgatagtaacaagatgtggaactcacagcagcattcttttttttctccttttgtttgcattcatagCATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCGCACAACAAGCCAAATTTGATTAAAGGTCTTCTTCCAGAGATATTACCTCTTCTATACG

Basic information

species Zea mays
transcript GRMZM2G168629_T04
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T01 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 24
gtaatgacacacttgtttacataatttattatttttcattatactgaat-gatagtaacaagatgtggaactcacagcagcattcttttttttctccttttgtttgcattcatagCATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCGCACAACAAGCCAAATTTGATTAAAGGTCTTCTTCCAGAGATATTACCTCTTCTATACG
              || |  | |||| |  |   ||||   |  | | |  ||  |  | ||||||||   |||               || | ||||||||      ||   |||| |||||  | ||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| ||||||||||| ||  |||| |||||| | || |
--------------gtatgga-aattaagcacagttcagcgtttttacttaatgctgtctagatgtggtgttca---------------ttgtttccttttgcac---tttgcagCACGTGAGGCGTGCAGCTGTGCTGGCCTTGAGTACAGCTGCCCACAACAAGCCAAATTTGATTAAGGGTCTTCTTCCTGAATTATTGCCTCTTTTGTATG
















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|33103242|gb|CF063202.1|CF063202
EST:     ACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGG                         CATGTGAGAAGAGCAGCAGTCCTGGCTTTGAGCACAGCAGCGCACAACAGG
genomic: ACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGGgtaatgacac ... gcattcatagCATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCGCACAACAAG
EST: gi|16746077|gb|BM032507.1|BM032507
EST:     TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAG-CAGCGATAGG                         CATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGC-CAGCAGCGC
genomic: TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGGgtaatgacac ... gcattcatagCATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCGC
EST: gi|18384939|gb|BM418138.1|BM418138
EST:     TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGG                         CATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCAGCACAA
genomic: TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGGgtaatgacac ... gcattcatagCATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGC-GCACAA
EST: gi|89761370|gb|DY689409.1|DY689409
EST:     TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGG                         CATGTGAGAAGAGCAGCAGTTCTGGC
genomic: TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGGgtaatgacac ... gcattcatagCATGTGAGAAGAGCAGCAGTTCTGGC
EST: gi|32931823|gb|CF036635.1|CF036635
EST:     TGCACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGG                         CATGTGAGAAGAGCAGCAGTCCTGGCTTTGAGCACAGCAGCGCACAACAAG
genomic: TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGGgtaatgacac ... gcattcatagCATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCGCACAACAAG
EST: gi|50322915|gb|CO518041.1|CO518041
EST:     TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGG                         CATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCGCACAACAAG
genomic: TGTACTCCAAGATATCTACTTTCTTGATGTTGATTAAAGACAGCGATAGGgtaatgacac ... gcattcatagCATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCGCACAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtggaactcacagcagcattcttttttttctccttttgtttgcattcatagCATGTGAGAAGAGCAGCAGTTCTGGCTTTGAGCACAGCAGCGCACAACAAGCCAAATTTGATTAAAGGTCTTCTTCCAGAGATATTACCTCTTCTATACG
        aactcac  putative branch site (score: 2)
                    cattcttttttttctc  putative PPT
                     attcttttttttct  TA-rich tract