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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagatgtatttgggatgaagggagtaggtcaagtttagtgcaattctttatttgccttttgttgtcgtatctgtgtttacttgtagtttattgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGATCCTGATGGTCTACTTATTGATGCAAACTCTGGAAAG

Basic information

species Zea mays
transcript GRMZM2G109039_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109039_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 3'ss of exon 8
tgagatgtatttgggatgaagggagtaggtcaagtttagtgcaattctttatttgccttttgt--tgtcgtatctgtgtttacttgtagtttattgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGATCCTGATGGTCTACTTATTGATGCAAACTCTGGAAAG
  |       |  | ||   | ||  |   | | |  | |||  |   |  |||   || |||  | | || ||    || | |  || |||  ||||||||||| |  | |||||||||||||||||| | | |||||||||||| ||||||||| ||||| |||| ||||| || || || ||||||
--atccaacatcagtatacggagatcaaaaccaatggaatgctttggatgttttagtttctgtactctggtctcacaattcattgttattttggtgatgcagCATACAGCATTGAGTCCTGACAGAAAGCTTGCTGTTATTGTGGGGGATGATCCTAATGGTTTACTAATTGACGCCAATTCAGGAAAG
















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|76290624|gb|DV030192.1|DV030192
EST:     AGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: AGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|166579805|gb|EG313295.1|EG313295
EST:     TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGG
genomic: TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGG
EST: gi|37401261|gb|CF637993.1|CF637993
EST:     -GAGAGATTTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: GGAGAGA-TTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|211395427|gb|FL283717.1|FL283717
EST:     TGAAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|211395430|gb|FL283720.1|FL283720
EST:     TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|22472113|gb|BU036593.1|BU036593
EST:     TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|60336793|gb|DN203766.1|DN203766
EST:     TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|21987570|gb|BQ779098.1|BQ779098
EST:     TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|60357769|gb|DN224742.1|DN224742
EST:     TCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: TCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|78178962|gb|DV549335.1|DV549335
EST:     CATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: CATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|37361241|gb|CF602530.1|CF602530
EST:     TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|71304856|gb|DR788543.1|DR788543
EST:     TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGT-G--GTTATTGTGGGTGATGAT
genomic: TGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
EST: gi|50334469|gb|CO529595.1|CO529595
EST:     TCAAGCATTTTCAGTTTGAATGGCCAGTGAAT                         CATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT
genomic: TCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttct ... attgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttatttgccttttgttgtcgtatctgtgtttacttgtagtttattgatgcagCATGCTTCGTTGAGTCCTGACAGAAAGGTGGTTGTTATTGTGGGTGATGATCCTGATGGTCTACTTATTGATGCAAACTCTGGAAAG
                                            tattgat  putative branch site (score: 3)
                                       tagtttatt  TA-rich tract