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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaattttctgtcgagtaagctttcttttgctttggggtaaaatgcttgcttttgtttgcaccattcaaaataatatggcttttgttttcag

Basic information

species Glycine max
transcript GLYMA13G16040.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G16040.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 5'ss of exon 31
AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtga-attttctgtcgagtaagctttcttttgctttggg---gtaaaatgcttgcttttgtttgcaccattcaaaataatatggcttttgttttcag
|| |||||||||||||| |||||||| ||||| ||||||||||| ||||||||||   | || ||||| || ||| | | ||| ||||| |      ||  ||    |      || | |    ||       |  ||    |    |  || |  |  ||| || |   ||     | |||||    
AGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAGgtaatcagtgttggctaataatggtttttgcgtacaattcaaaactggcaagaaataatctgagtgtttaagatttaagagtgta-aatatctgtttattt

upper sequence: GLYMA13G16040.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G303655_T01 (Zea mays), 5'ss of exon 20
AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaa--ttttctgtcg-------agt-aagctttcttttgctttggg-gtaaa---atgcttgcttttgtttgcaccattcaaaataatatggcttttgttttcag
 | |||||||| |||||||||||||| ||||| |||||||||||||| ||||| |   |  | ||| | || ||  |   ||| |||||  |  |   | |||||| |       ||| |||      |||| | ||    | ||   || | || |||||||||   | |||    ||   |  || | |       
CGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAGgtatgcaatgctattctgttgtgaaatgagtgaagtagatgtttgatgtgtccatgaacttattcatggttttgtttgtgtccttc----tagctttactctcg-------

upper sequence: GLYMA13G16040.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G014805_T02 (Zea mays), 5'ss of exon 12
AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtga----attttctgtcg---agtaagctttcttttgctttggggtaaaatgcttgcttt--tgtttgcaccattcaaaataatatggcttttgttttcag
|| |||||||| |||||||||||||| ||||| |||||||||||||| || || |   |  | ||||| || ||  | | ||| |||||  |  |    || |||||| |   | | ||     |     || |  ||   | | |||      || |||      |   |   ||   ||   | |      
AGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACCGATACAACATCGAAAAGGTCTTACACAGCCAATCAGgtaggcaatgctatattctgttgtaaaatgagtgaaataaatgttcgacgttgtaagattgtggaagtgcttgattgtattgcatagatggagcacatat------

upper sequence: GLYMA13G16040.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 5'ss of exon 31
AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaattttctgtcgagtaagctttcttttgctttggggtaaaatgcttgcttttgtttgcaccattcaaaataatatggcttttgttttcag
||||||||||||||||||||||||||||| ||||||||  | |||||| |||||| ||||||||||||  | ||||| |  || |||||  ||   || |  ||  | |||  | | |  || || |     | ||||| | || |   | |   |||    ||  | |  |       | |||
AGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAGgtatgttgcttcttggt--attaacttctatcctgtttag-----atatgctagattgtaaattccatatt---gatgttgtcacccaaccatgcag

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|13788778|gb|BG651369.1|BG651369
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG                         AATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaat ... ttgttttcagAATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
EST: gi|214006038|gb|DB990447.1|DB990447
EST:     AGCATACTGACAATGCTCCTAAAAGATCATATGCTGGCCACCAG                         ATTTTTTACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
genomic: AGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaat ... ttgttttcagAATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
EST: gi|58015534|gb|CX702276.1|CX702276
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG                         AATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaat ... ttgttttcagAATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
EST: gi|58015738|gb|CX702480.1|CX702480
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG                         AATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaat ... ttgttttcagAATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
EST: gi|209699336|gb|BW664055.1|BW664055
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG                         AATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaat ... ttgttttcagAATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
EST: gi|57573985|gb|CX546960.1|CX546960
EST:     GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG                         AATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT
genomic: GCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaat ... ttgttttcagAATCGCCACACATTTGAGAAGCCAGTAAAGATTTATAATTAGGAAACTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAGgttagtgaattttctgtcgagtaagctttcttttgctttggggtaaaatgcttgcttttgtttgcaccattcaaaataatatggcttttgttttcag

- - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG