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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagactttttatttttatttttgcataacatcattgataatttattctggttctcgtgttacgtagttatggttgtgtttagggtggctaaaagatgggaaataattaattcaaactctggtgacaggactgttggatggaaaatactaactgaatttttttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAGGTTTTG

Basic information

species Glycine max
transcript GLYMA20G22600.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22600.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 6
gtatagactttttatttttatttttgcataacatcattgataatttattctggttctcgtgttacgtagttatggttgtgtttagggtggctaaaagatgggaaataattaattcaaactctggtg-acaggactgttggatggaaaatactaactgaatttttttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAGGTTTTG
                                                                   |||     | || |  |   ||  | || |||  ||  |  | | | || | |    || |||    ||||  |   ||||     | |   || || |||||| |||| |||||||| || |||||| ||||  |||||||||||||||||||||| || |||
-----------------------------------------------------------------acagtcgca-tagtttccatattg--ttaatgatatgagtttgt-attccacattgcaatgcacaattttgttcaagtaaaaa-----attttgttcttctctgtgtagGTGAATCCACATACCCACCAGCTTAAGCTATGTGACTTTGGAAGTGCAAAAGTCTTG
















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|6566240|gb|AW233921.1|AW233921
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|12773850|gb|BG238777.1|BG238777
EST:     ATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGATAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|208162047|gb|GD960160.1|GD960160
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGG
EST: gi|19052551|gb|BM731218.1|BM731218
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|15287684|gb|BI471575.1|BI471575
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|209699787|gb|BW655800.1|BW655800
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAAGTGCAA-
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAA-GTGCAAA
EST: gi|14990268|gb|BI315941.1|BI315941
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|27426708|gb|CA938228.1|CA938228
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|11413300|gb|BF425311.1|BF425311
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|192296530|gb|FG991636.1|FG991636
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|16997007|gb|BM086379.1|BM086379
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|208183454|gb|GD981508.1|GD981508
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|15000029|gb|BI320843.1|BI320843
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|192321549|gb|FK012899.1|FK012899
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|193377439|gb|FK339255.1|FK339255
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|14990090|gb|BI315763.1|BI315763
EST:     ATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|254333709|gb|GR848627.1|GR848627
EST:     ATCGTTGTATTG-AGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACA
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACA
EST: gi|120492579|gb|EH220746.1|EH220746
EST:     TCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: TCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|9205156|gb|BE331380.1|BE331380
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|254327042|gb|GR836651.1|GR836651
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAG
EST: gi|22525150|gb|BU083970.1|BU083970
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
EST: gi|13481244|gb|BG510587.1|BG510587
EST:     ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTG                         GTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG
genomic: ATCGTTGTATTGGAGTCTGCCATCGGGATATCAAGCCTCAAAATCTATTGgtatagactt ... ttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctggtgacaggactgttggatggaaaatactaactgaatttttttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAGGTTTTG
                             tactaac  putative branch site (score: 0)
                                        tttttttctgt  putative PPT
                         aaaatactaactgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagactttttatttttatttttgcataacatcattgataatttattctggttctcgtgttacgtagttatggttgtgtttagggtggctaaaagatgggaaataattaattcaaactctggtgacaggactgttggatggaaaatactaactgaatttttttctgtgcagGTCAATCCACACACTCACCAGGTTAAATTATGTGACTTTGGAAGTGCAAAGGTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG