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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttattgtatcatctagaaattgaaattgaaatgttttaccaagctttctagttctattttaatatgtttacattttctcttttaattatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTGTTTCTATATATGATAGCTCCTCTGGTAAGAAGGTTGGTGTGGGGGCCTT

Basic information

species Glycine max
transcript GLYMA11G07910.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G51130.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatttattgtatcatctagaaattgaaattgaaatgttttaccaagcttt--ctagttctattttaatatgtttacattttctcttttaattatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTGTTTCTATATATGATAGCTCCTCTGGTAAGAAGGTTGGTGTGGGGGCCTT
       ||   || |||    | |  | |  || | | ||   |   |||  || || | || |  |  |  | | ||||| | || |  ||   | || || | | || || |||||||| ||||| ||||| ||||| |||||||| || ||||||||||| | |||   ||  || || |||||||| ||    ||
------gtttgttcttctccggactccagtgaaattttgtttatattttttgtcttgtccgatatctaacttctcagatttttttttctcctttacaaagCGGCACTACCGTTAGAGTTTCCAGATGGCACCACACCAGTAACATGCCGGGTCTCTATATATGACAACTCAAGTGACAAAAAAGTTGGTGTCGGAAAATT

upper sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 6
gtatttattgtatcatctagaaattgaaattgaaatgttttaccaagctttctagttctattttaatatgtttacattttctcttttaattatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTGTTTCTATATATGATAGCTCCTCTGGTAAGAAGGTTGGTGTGGGGGCCTT
         ||||||| |  | | |          ||       |    | ||   || ||||   ||| || ||   |  | | |||      |||| ||| ||||| || ||||| || ||||| || || ||||||||||||||||| |||||||||||||| ||  | |  |  ||||||||||||||  ||| 
---------gtatcatatcaataat----------tgcccacttacatctacttaatcaatttgtttattttcac---taatgtattatccccaacagCGGAGTTGCCTTTAGAGTTCCCAGATGGTACTACTCCAGTTACATGCCGTGTGTCTATATATGATAGTTCTACAGACAGTAAGGTTGGTGTGGGATCCTC
















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|207846669|gb|GD819994.1|GD819994
EST:     TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAG                         TGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
genomic: TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAGgtatttattg ... attatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
EST: gi|13791595|gb|BG654186.1|BG654186
EST:     TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAG                         TGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
genomic: TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAGgtatttattg ... attatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
EST: gi|23052777|gb|BU577268.1|BU577268
EST:     TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAG                         TGGAATTGCCATTGGAGTTTCCTGATGGGAC
genomic: TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAGgtatttattg ... attatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGAC
EST: gi|7233548|gb|AW568953.1|AW568953
EST:     TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAG                         TGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
genomic: TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAGgtatttattg ... attatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
EST: gi|207846938|gb|GD819479.1|GD819479
EST:     TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAG                         TGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
genomic: TGCATTTCCTATTCCAAGTCAATTTACAGACTGCTGTCATGACGGGGGAGgtatttattg ... attatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
EST: gi|120533133|gb|EH261266.1|EH261266
EST:     ACAGACTGCTGTCATGACGGGGGAG                         TGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
genomic: ACAGACTGCTGTCATGACGGGGGAGgtatttattg ... attatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
EST: gi|120533498|gb|EH261631.1|EH261631
EST:     ACAGACTGCTGTCATGACGGGGGAG                         TGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG
genomic: ACAGACTGCTGTCATGACGGGGGAGgtatttattg ... attatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagctttctagttctattttaatatgtttacattttctcttttaattatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTGTTTCTATATATGATAGCTCCTCTGGTAAGAAGGTTGGTGTGGGGGCCTT
                                        ttttaat  putative branch site (score: 3)
                                 ttttctcttttaatt  CT-rich tract
            ttctattttaatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttattgtatcatctagaaattgaaattgaaatgttttaccaagctttctagttctattttaatatgtttacattttctcttttaattatgacagTGGAATTGCCATTGGAGTTTCCTGATGGGACCACGCCAGTTACATGCCGTGTTTCTATATATGATAGCTCCTCTGGTAAGAAGGTTGGTGTGGGGGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG