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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtatttggttaactgaaccttgtcaggcacattattgtgaaaagtttattatgttttctcttcagatgggatcagcttcttctggttttaaccatctacatatgatttttttttctaataacaGGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAAATTTGTTGGAGATGGATATACCCACTGTGAA

Basic information

species Glycine max
transcript GLYMA18G44580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 6
ggtatttggttaactgaaccttgtcaggcacattattgtgaaaagtttattatgtt-ttctcttcagatgggatcagcttcttctggttttaaccatctacatatgatttttttttctaataacaGGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAAATTTGTTGGAGATGGATATACCCACTGTGAA-
                                       | |    ||||  |||| |  ||||||||       | ||| | |    | |  | ||  | ||   | ||   | | ||     |||||||||| || |||||||| |||||||| ||| ||||  ||  ||| ||||||||||| ||||| || || ||||||||| 
---------------------------------------gtatttcttatggtgttatcttcttcaga-------aacttttcca---tctggctatgcatatcatacttggctgtgtacgtgtagGACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTGAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAG

upper sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 6
ggtatttggttaactgaaccttgtcaggcacattattgtgaaaagtttattatgtt-ttctcttcagatgggatcagcttcttctggttttaaccatctacatatgatttttttttctaataacaGGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAAATTTGTTGGAGATGGATATACCCACTGTGAA-
                                       | |    ||||  |||| |  ||||||||       | ||| | |    | |  | ||  | ||   | ||   | | ||     |||||||||| || |||||||| |||||||| ||| ||||  ||  ||| ||||||||||| ||||| || || ||||||||| 
---------------------------------------gtatttcttatggtgttatcttcttcaga-------aacttttcca---tctggctatgcatatcatacttggctgtgtacgtgtagGACACTTTTCGTGGAAGAGTTTGTGAATGTCCAGTTGTAAAAGGTGTTAAATTTGTTGGTGATGGCTACACTCACTGTGAAG

upper sequence: GLYMA18G44580.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G30290.2 (Arabidopsis thaliana), 3'ss of exon 7
ggtatttggttaactgaaccttgtcaggcacattattgtgaaaagtttattatgttttctcttcagatgggatcagcttcttctggttttaaccatctacatatgatttttttttctaataacaGGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAAATTTGTTGGAGATGGATATACCCACTGTGAA-
                               | ||   | | || |||    | |||| | | ||  |   ||||          |  ||||     |   ||| ||||| || |    |   ||||||||||| |||||||||||||| |||| || |||||||||  ||| || ||| | || || || ||||| || |||||| 
-----------------------------gtactaaaataagaacttt----tattttgt-tacaatttatatcaa---------gccttaaa---atgagtattattttcttgtaatgttttagGACACTTTCAGAGGAAGAGTATGTCAATGTCCCATTGTTCAAGGTGTCAAGTTTCTCGGTGACGGTTATACACATTGTGAAG

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|20497891|gb|BQ272821.1|BQ272821
EST:     AACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG                         GGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAA
genomic: AACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAGggtatttggt ... tctaataacaGGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAA
EST: gi|13478328|gb|BG507848.1|BG507848
EST:     AACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAG                         GGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAA
genomic: AACAATGGTGGTTGTTGGCAGGACAAATCTTCTAACATTACTGCATGCAGggtatttggt ... tctaataacaGGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatcagcttcttctggttttaaccatctacatatgatttttttttctaataacaGGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAAATTTGTTGGAGATGGATATACCCACTGTGAA
                                            ttctaat  putative branch site (score: 2)
                                  tgatttttttttct  CT-rich tract
                         atctacatatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatttggttaactgaaccttgtcaggcacattattgtgaaaagtttattatgttttctcttcagatgggatcagcttcttctggttttaaccatctacatatgatttttttttctaataacaGGACACTTTCCGAGGAAGAGTATGTGAATGCCCAATTGTTCAAAATGTGAAATTTGTTGGAGATGGATATACCCACTGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA