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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattctcctactagtgcgttttgatttgatggcgatcatgagattgttgttcttgattttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAACAAAGAGCCGCGTTGAATATTGGAATCGGTTGGAGGGGTTTGAATGAGG

Basic information

species Glycine max
transcript GLYMA20G38780.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G155580_T03 (Zea mays), 3'ss of exon 1
---------------------------gtaatattctcctactagtgcgttttgatttgatggcgat-catgagattgttgttcttgattttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAACAAAGAGCCGCGTTGAATATTGGAATCGGTTGGAGGGGTTTGAATGAGG
                            ||| |   |  ||    |    | |  ||  ||   ||    | ||  |  | || |||    | | |  |||||||||| || ||||| |||||||||||||| |||| ||| ||||| ||  |  | || || || || || || || || |||||||| |||||   | 
atgatgctgtttatcatgcctaagtgcctaacaacttaatatgtatattgtatacttgtatattgacattttagtctcatattgttgtcacttgatacagGGATTCACAACATATGCTGAGAGGAGGATTGTTGAGGTTGTGCAAGGGGAGGAGCGGGCAGCCTTAAACATGGGGATTGGATGGAGGGGATTGAACAGGA

upper sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g03300.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------gtaatattctcctactagtgcgttttgatttgatggcgatcatgagattgttgttcttgattt-tggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAACAAAGAGCCGCGTTGAATATTGGAATCGGTTGGAGGGGTTTGAATGAGG
                              |  | ||      | |   ||   |  | |||     | ||    || ||  | || |||| || ||  |||| || || |||||||| ||| |||| ||||| |||||||| ||||| ||  | || || ||  ||||||||||||| ||||||||||| ||||||||||
cttaatcattttctgactaatttttggttgaggagtccaagttttgcatgtacaggatagatttttgt-atctttttatttatgttaatttatgtttccagGGTTTTACAACTTATGCAGAGCGGAGAATTGTTGAGGCTGTGCAAGGGGAGGATAGGGCTGCTCTGAATATTGGAATTGGTTGGAGGGGATTGAATGAGG
















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|193691469|gb|FK628424.1|FK628424
EST:     CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTNAATGAG                         GGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
genomic: CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAGgtaatattct ... ttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
EST: gi|298164042|gb|HO013687.1|HO013687
EST:     CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAG                         GGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
genomic: CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAGgtaatattct ... ttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
EST: gi|7691304|gb|AW759497.1|AW759497
EST:     CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAG                         GGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
genomic: CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAGgtaatattct ... ttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
EST: gi|208183402|gb|GD982842.1|GD982842
EST:     CTGGGAATTTGATCACTAACAAGACCAACGAACATTTCTGGTTGAATGAG                         GGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGT
genomic: CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAGgtaatattct ... ttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGT
EST: gi|254326546|gb|GR841138.1|GR841138
EST:     CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAG                         GGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
genomic: CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAGgtaatattct ... ttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
EST: gi|193477294|gb|FK441821.1|FK441821
EST:     CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAG                         GGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCT
genomic: CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAGgtaatattct ... ttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCT
EST: gi|19270287|gb|BM886543.1|BM886543
EST:     CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAG                         GGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA
genomic: CTGGGAATTTGATCACTAACAAGACCAATGAACATTTCTGGTTGAATGAGgtaatattct ... ttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcgttttgatttgatggcgatcatgagattgttgttcttgattttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAACAAAGAGCCGCGTTGAATATTGGAATCGGTTGGAGGGGTTTGAATGAGG
                                     tcttgat  putative branch site (score: 4)
     ttttgattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattctcctactagtgcgttttgatttgatggcgatcatgagattgttgttcttgattttggttttagGGATTCACTACTTATGCGGAGAGGAGGATTGTGGAGGCTGTCCAAGGAGAACAAAGAGCCGCGTTGAATATTGGAATCGGTTGGAGGGGTTTGAATGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG