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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTATGACATGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttctttggtttcttagctatttctgttaccttaatgttctatatttggatcttcttgttggtgctattattacaaggtacatctttctacacat...

Basic information

species Zea mays
transcript GRMZM2G109039_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109039_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 5'ss of exon 8
CGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTATGACATGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttctttggtttcttagctatttctg---ttaccttaatgttctatatttggatcttcttgttggtgctattattacaaggtacatctttctacacat
 ||||||||||||||||| ||||| ||||||||||| ||| ||||||| |||||||| || ||||| | |||||||||||||||||||||||||||||||||| || | ||| |||| || |  |   ||    ||   | ||  | ||||| || |    |   |   ||   ||| |    |  | |||  ||  |||   
TGTTCACTTCATGGCATCGAATAATGACTCTGGTGTAAGAGACTATGATATGGAGAGGTTTCAGCTCTACAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaagtcttttttgtttatttgtgacaccttgcttttggtaaacctactataattagggtat---gcatgtatgattgtgtagacattcataatttcacattg

upper sequence: GRMZM2G109039_T04 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G12980.2 (Glycine max), 5'ss of exon 8
CGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTATGACATGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttctttggtttcttagctatttctgttaccttaatgttctatatttggatcttcttgttggtgctattattacaaggtacatctttctacacat---------
 ||||| |||||||| ||||| || |||||||| || ||| ||| ||| ||||||||||| ||||| |  ||||||||    |||   |||||||| |||||| ||   |    |||  |     ||||  |    | |||  |  ||||   ||  || || ||  |  | || ||    |||| || | | || | ||         
TGTTCATTTCATGGCTTCAAACAATGACTCTGGAGTTAGAGACTTTGATATGGAGAGATTTCAGCTTTCGAAGCATTTCTGCTTTCCTTGGCCAGTAAATgtaagtacttccactttgat-----tttccatgttttaaataatagatat---gacatttttattattattgtt-ttgatgggtatatatatatatatattgctttatc
















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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTTCACTTCATGGCATCAAATAACGACTCTGGTGTGAGATACTATGACATGGAGAGATTCCAGCTATTCAAGCATTTTCAGTTTGAATGGCCAGTGAATgtaggtttctttggtttcttagctatttctgttaccttaatgttctatatttggatcttcttgttggtgctattattacaaggtacatctttctacacat

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA