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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagttacaatcacaatttggtgtctttttaatgtcagtaatagccatgaaaactagtgcttctatcgtaagagaaaagacaaagaagaaaaaaa...

Basic information

species Glycine max
transcript GLYMA09G28040.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28040.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G25370.1 (Arabidopsis thaliana), 5'ss of exon 3
AGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagttacaatcacaatttggtgtctttttaatgtcagtaatagccatgaaaactagtgcttctatcgtaagagaaaagacaaagaagaaaaaaa
|| |||||||| ||   ||||||||| |||||||| || |||||||||||||||||||  || || ||||| || ||||||||||| ||||| || |||||||||| | |   |  |  |  || |  ||   ||  |||        | | |  |   |||   ||   |  ||||    |  |    |      | | 
AGAGCTATAAAGTCACTTGCAATGGGAGAATTGGAGGCTAGGAAGCTCAAGTATCCAAGTACCGGGACCGAAGCCATTCTCATGGGTATTTTAGTCGAAGgtttgtgattctgagacctatatttgcttcagctttgtgttttgccgcgtcttctagtttagattttgatttctaaggatcactatgttgctttggatat

upper sequence: GLYMA09G28040.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0022g01840.t01 (Vitis vinifera), 5'ss of exon 3
AGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagttacaatcacaatttggtgtctttttaatgtcagtaatagccatgaaaactagtgcttctatcgtaagagaaaagacaaagaagaaaaaaa--
||||| ||||| || | | | |||| |||||||||||| |||||||| ||||| ||||| || |||||||||||  |||| ||||| || |||||||| |||| || | ||    |||||  ||   |  |  | | |||    | | |   |  | | |  |||   | |     |    |||       || |   |   
AGGGCAATAAAGTCATTTTCTATGGCGGAATTGGAAGCAAGGAAGCTGAAGTACCCAAATACTGGAACCGAGGCTCTTCTAATGGGAATCTTGGTTGAGGgttagt-aattttggtcacatcttttaggttgatcactgttcacatttgtgttttaga-tgttgcagttttttcttgttgcaagctgtttcagcatggactc
















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|14990401|gb|BI316074.1|BI316074
EST:     GTATCCAAACACGGGAACCGGGGCGATTCTCATGGGGATTTTGGTTGAAG                         GAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
genomic: GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagt ... ttctttccagGAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
EST: gi|4284742|gb|AI440819.1|AI440819
EST:     GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAG                         GAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
genomic: GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagt ... ttctttccagGAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
EST: gi|6848038|gb|AW350328.1|AW350328
EST:     GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAG                         GAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
genomic: GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagt ... ttctttccagGAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
EST: gi|298183306|gb|HO028519.1|HO028519
EST:     GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAG                         GAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
genomic: GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagt ... ttctttccagGAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
EST: gi|7589480|gb|AW705253.1|AW705253
EST:     GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAG                         GAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
genomic: GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagt ... ttctttccagGAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
EST: gi|23064459|gb|BU579232.1|BU579232
EST:     GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAG                         GAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
genomic: GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagt ... ttctttccagGAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
EST: gi|24135410|gb|BU925920.1|BU925920
EST:     GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAG                         GAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA
genomic: GTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagt ... ttctttccagGAACAAGTAATGCTGCAAAATTCTTAAGAGCTAATGGAATTACTCTTTTGA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGCTATAAAATCGTATGCAATGGGGGAATTGGAAGCGAGGAAGCTCAAGTATCCAAACACGGGAACCGAGGCGATTCTCATGGGGATTTTGGTTGAAGgtttgttagttacaatcacaatttggtgtctttttaatgtcagtaatagccatgaaaactagtgcttctatcgtaagagaaaagacaaagaagaaaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gacaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaaa