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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTGACATGGAACGGGCAGAAGGAGATACCGGTGGGGAATTTGACCCGCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgagttcgtctttcctgatcaattcagatctaggcctctacagtgacgctaggctgtattttgattccaccatccgctggttcttcag

Basic information

species Zea mays
transcript GRMZM2G029566_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G029566_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g10310.1 (Oryza sativa), 5'ss of exon 13
GGAGCTGACATGGAACGGGCAGAAGGAGATACCGGTGGGGAATTTGACCCGCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgagttcgtctttcctgatcaattcagatctaggcctct-----------acagt----------gacgctaggctgtattttgattcca-ccatccgc-tggttcttcag
|||||| |||||||| ||||||||||||||| | || || || | |||||||||||||||||||||||| ||||| |||||||||||||  ||||||||||||| |  |  || |   || |||||||  || || |||  ||||           |||            ||  | | ||| ||| ||||| ||| |||||  | || || | |||
GGAGCTAACATGGAATGGGCAGAAGGAGATATCAGTTGGAAACTCGACCCGCAAGTTCCTAGAAGATGGGGATGAGGTCATCTTGACAGCTTGTTGCAAGgtacagcaatctcataagtcttgatcaaaccaaatttagagctcttttcgtctaaaacaaatatctttgaagattccatgctctatcttgatgccatccatctacatgtttttacag

upper sequence: GRMZM2G029566_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA15G12100.1 (Glycine max), 5'ss of exon 13
GGAGCTGACATGGAACGGGCAGAAGGAGATACCGGTGGGGAATTTGACCCGCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgt-actgtgagttcgtctttcctgatcaattcagatctaggcctctacagtgacgctaggctgt--attttgattccaccatccgctggttcttcag-----------
 ||  | || ||||| || || || | | |||| |||      || |     || || || ||||||||||||||||| ||||| || |||| ||||||||| ||  | | ||    | | |  | |   || | | |      ||| | ||  | ||   | |   ||||  ||     ||  | | ||| ||||            
AGAATTAACGTGGAATGGACAAAACGCGGTACCAGTGAATGGGTTAAATAAGAAATTTCTTGAAGATGGAGATGAAGTTATCTTAACTGGATATTGCAAGgttacaatcaattaagatcttc--aacgcctctgttttg-----ctaaaatgctgttatcttttcagtttttcttgagagatttgttagtt-ttcatttcccagtatc

upper sequence: GRMZM2G029566_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA09G01270.2 (Glycine max), 5'ss of exon 12
GGAGCTGACATGGAACGGGCAGAAGGAGATACCGGTGGGGAATTTGACCCGCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgta-ctgtgagttcgtctttcctgatcaattcagatctaggcctctacagtgacgctaggctgtattttgattccaccatccg---ctggttcttcag--
 ||  | |||||||| || || ||     |  | |||    | || |  || || || || ||||||||||| ||||||||||| || |||| |||||||||| |  | | ||    | | |    |   |       | |  |    | |    | |   |  ||    | |     |   |   ||  || || |   
AGAATTAACATGGAATGGACAAAACACAGTGTCAGTGAATGAGTTAAATCGGAAATTTCTTGAAGATGGAGACGAAGTCATCTTAACTGGATATTGCAAGgtaacaatcaattaagatcttcaatgcctcttttgcaaaagtgttgtaattttttcaacttttcatgagaaatttcttagttgtatctaatttttaactg

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|110933692|gb|EE153918.1|EE153918
EST:     AAGTTCCTAGAAGATGGAGATGGAAGTCATCTTGACAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: AAGTTCCTAGAAGATGGAGAT-GAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|89764160|gb|DY691068.1|DY691068
EST:     CAAGTTCCTAGAAGATGGAGATGAAGTCATCTAGAGCAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: CAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGA-CAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|211273149|gb|FL031472.1|FL031472
EST:     GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|33096207|gb|CF056201.1|CF056201
EST:     GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|113704214|gb|EE681718.1|EE681718
EST:     TGGAGATGAAGTCATCTTGACAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: TGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|116829718|gb|EC871187.1|EC871187
EST:     GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAT                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|211273147|gb|FL031470.1|FL031470
EST:     GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|211274945|gb|FL031473.1|FL031473
EST:     GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|76908479|gb|DV162961.1|DV162961
EST:     GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|76294227|gb|DV033795.1|DV033795
EST:     GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAG                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
EST: gi|116829759|gb|EC871644.1|EC871644
EST:     GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAT                         GGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG
genomic: GCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgag ... ggttcttcagGGTGAAGGCTACAACATTGGTTTTGGAACCTGCACCGGGAAGGTTCTGCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCTGACATGGAACGGGCAGAAGGAGATACCGGTGGGGAATTTGACCCGCAAGTTCCTAGAAGATGGAGATGAAGTCATCTTGACAGGATGTTGCAAGgtactgtgagttcgtctttcctgatcaattcagatctaggcctctacagtgacgctaggctgtattttgattccaccatccgctggttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG