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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagtccagacatttgtgtatctaggagtatgacttatttattgttagaaaaatgtaaatccagttccagacttctgtttaccataactgaagaaatgcaaatttgcag

Basic information

species Glycine max
transcript GLYMA10G35960.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35960.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 5'ss of exon 5
GGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagtccagacatttgtgtatctaggagtatgacttatttattgttagaaaaatgtaaatccagttccagacttctgtttaccataactgaagaaatgcaa-atttgcag
|||||||| ||||| ||||||||||| || || || ||||| || || ||||||||||| ||||| ||||||| ||| |||||||||  |   |||  | || | | |  | |     |  | || |  |   |  |     | |  ||  | ||      ||||   |||     |||   | |||||| || |||||
GGAGCAATCATGGCGGTTGGAGCATCAGAACCAACCGTTGTTGCCACCAAGGATGGTCGGATTGGCATGAAGAGCCAGATGCAGgta--attttccttagatctctctccccaaattgagaatttctacaccatgtg-----tttggatttattttacagtttct---tac----gctgggaacatgcaatatctgcag
















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|22928634|gb|BU545773.1|BU545773
EST:     GGTCGCATTGGAATGAAGAACCAAATGCAG                         GTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
genomic: GGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagt ... aaatttgcagGTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
EST: gi|193397613|gb|FK365075.1|FK365075
EST:     CTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG                         GTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
genomic: CTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagt ... aaatttgcagGTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
EST: gi|7691722|gb|AW759844.1|AW759844
EST:     GGTCGCATTGGAATGAAGAACCAAATGCAG                         GTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
genomic: GGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagt ... aaatttgcagGTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
EST: gi|10844471|gb|BF071007.1|BF071007
EST:     GTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG                         GTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
genomic: GTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagt ... aaatttgcagGTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
EST: gi|193636258|gb|FK580767.1|FK580767
EST:     GGAATGAAGAACCAAATGCAG                         GTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCG
genomic: GGAATGAAGAACCAAATGCAGgtatgagagt ... aaatttgcagGTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
EST: gi|193604520|gb|FK555915.1|FK555915
EST:     CTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG                         GTCAATGTTACTGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
genomic: CTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagt ... aaatttgcagGTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
EST: gi|193417002|gb|FK382036.1|FK382036
EST:     CTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG                         GTCAATGTTACCGCTGATCATCGAAGTAAATAACTATGGTGCT
genomic: CTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagt ... aaatttgcagGTCAATGTTACCGCTGATCATCGA-GTAA-T--CTATGGTGCT
EST: gi|193609247|gb|FK561159.1|FK561159
EST:     CTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAG                         GTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA
genomic: CTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagt ... aaatttgcagGTCAATGTTACCGCTGATCATCGAGTAATCTATGGTGCTGATTTGGCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCAATAATGGCTGTTGGAGCATCGGAGCCCACTGTTGTGGCTACAAAGGATGGTCGCATTGGAATGAAGAACCAAATGCAGgtatgagagtccagacatttgtgtatctaggagtatgacttatttattgttagaaaaatgtaaatccagttccagacttctgtttaccataactgaagaaatgcaaatttgcag

- - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC