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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATTATGAGGCCTATGTTCGGAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctccaatccatctctttcacagacacgcacttgaatagcccttgtgcagaaattattacatggtccaagattactatggtcctgtctaacctca...

Basic information

species Glycine max
transcript GLYMA11G37250.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37250.1 (Glycine max), 5'ss of exon 18
lower sequence: AC196072.3_FGT001 (Zea mays), 5'ss of exon 2
GTGATTATGAGGCCTATGTTCGGAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctccaatccatctctttcacagacacgcacttgaatagccctt-gtgcagaaattattacatggtccaagattactatggtcctgtctaacctca
||  | ||| | |||||||| || |||||||| |||||||| |||||  | || ||||| ||||||||||||| |  | |    ||   |||  |||   | |   ||||      |  ||    | || |  ||   |      || ||||||| || |  || |     | 
GTTGTGATGCGACCTATGTTTGGTGCATTTGGAAAGGCTGGAAGTTCCAATTCAATTGCATTTGTGAGCAAGgtagtgtttggttctgcctcaatcaagaaaaatgactttctcgacttttcaaactgataaaatataagtacaaaaaattactaagggctagtttggaaac-

upper sequence: GLYMA11G37250.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 5'ss of exon 17
GTGATTATGAGGCCTATGTTCGGAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatgg-ctccaatccatctctttcacagacacgcacttgaatagcccttgtgcagaaattatt--aca----tggtc-caagattac-tatggtcctgtctaacctca-------
||||| ||||| || ||||| |||||||||||||||||||| ||| |  |||| ||||||||||| |||||||||||  |  |  ||  ||||| || |   | | | ||        |  | |  |  ||| |||  |||    | ||   || | ||| || | |  | |      |||       
GTGATGATGAGACCCATGTTTGGAGCATTTGGCAAGGCTGGAAGTGCCAACTCTATTGCTTTTGTCAGCAAGgcatgaacatctctctctctctctctctctctctctctctctctctctatttctaataataattcaacaacaatagtaataataatacataagctttttttccctttcatcaacag
















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|31475006|gb|CD417034.1|CD417034
EST:     GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG                         GCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
genomic: GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctcc ... tcacaagcagGCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
EST: gi|8283731|gb|BE021290.1|BE021290
EST:     GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG                         GCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
genomic: GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctcc ... tcacaagcagGCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
EST: gi|12687960|gb|BG154235.1|BG154235
EST:     GGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG                         GCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
genomic: GGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctcc ... tcacaagcagGCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
EST: gi|27425580|gb|CA937100.1|CA937100
EST:     GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG                         GCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
genomic: GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctcc ... tcacaagcagGCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
EST: gi|7590807|gb|AW706551.1|AW706551
EST:     GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG                         GCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
genomic: GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctcc ... tcacaagcagGCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
EST: gi|16345257|gb|BI970852.1|BI970852
EST:     GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG                         GCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
genomic: GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctcc ... tcacaagcagGCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
EST: gi|16345254|gb|BI970849.1|BI970849
EST:     GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG                         GCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
genomic: GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctcc ... tcacaagcagGCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
EST: gi|16277034|gb|BI942169.1|BI942169
EST:     GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAG                         GCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG
genomic: GAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctcc ... tcacaagcagGCAGCTTTGGACGAAGGGGTGAAAGCTTCATATGGACTTAACAAGAGGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATTATGAGGCCTATGTTCGGAGCATTTGGCAAGGCTGGTAGTTCACACTCCATTGCTTTTGTGAGCAAGgcatggctccaatccatctctttcacagacacgcacttgaatagcccttgtgcagaaattattacatggtccaagattactatggtcctgtctaacctca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatctct