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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttattggtgaggaattaggacatttaactttgattttatgcctaatcataatatattattgtaagggcttattggtatgttgatctgtcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAATTATAAGCCACCTGGGATTTCTGTTTAGCTTGGAGCTGAATGTCATGACA

Basic information

species Glycine max
transcript GLYMA14G24270.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G24270.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 6
ggcttattggtgaggaattaggacatttaactttgattttatgcctaatcataatatattattgtaagggcttattggtatgttgatctgtctt-----ctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAATTATAAGCC---ACCTGGGATTTCTGTTTAGCTTGGAGCTGAATGTCATGACA
   |  ||       |  || || |    |     || ||||    ||   |  | | || || |      ||  |   || || |||||  |      || |||||| |||| |||||||||||| ||||| || || |||||||||||||||  | |   |    | |||  | ||          |  | ||| || |  |    
---tagttcacattaa--taagatagcagatgggtatattattttcaacatttttttttttttatggtcaattggttccattttaatctgcttctattgctacagCACACCAACTGAAGTGAAGGAGAGGATCTTAAAAGGAAGGATGGATTGACCTTTCTCCACAGAGCTGATAGTTGATCCCCTTCTATATCTGCATTTGGTT---
















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|192318541|gb|FK011365.1|FK011365
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAA-TGAAGTGA
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGA
EST: gi|151405517|gb|EV275331.1|EV275331
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|6914510|gb|AW396040.1|AW396040
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGAGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAAGAAAGGATTTTGGAAGGGAAG
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTG-AAGGGAAG
EST: gi|208035018|gb|GD836888.1|GD836888
EST:     GGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: GGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|37995705|gb|CF807294.1|CF807294
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|192331116|gb|FK020336.1|FK020336
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|208155706|gb|GD958467.1|GD958467
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|9819697|gb|BE555210.1|BE555210
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|193653839|gb|FK595651.1|FK595651
EST:     TGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: TGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|151410578|gb|EV280393.1|EV280393
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|193441805|gb|FK407742.1|FK407742
EST:     GGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: GGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|193585701|gb|FK538525.1|FK538525
EST:     GGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: GGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|23726885|gb|BU761446.1|BU761446
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTCTTGAAGGGA-GGATGGAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATT-TTGAAGGGAAGGATGGAT
EST: gi|17519828|gb|BM188870.1|BM188870
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGAT
EST: gi|26059647|gb|CA802561.1|CA802561
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGAT
EST: gi|207811930|gb|GD783515.1|GD783515
EST:     GAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: GAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|7233908|gb|AW569250.1|AW569250
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAAT
EST: gi|7926292|gb|AW832318.1|AW832318
EST:     TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT                         CACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGAT
genomic: TCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGTgtaagcttac ... tcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcataatatattattgtaagggcttattggtatgttgatctgtcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAATTATAAGCCACCTGGGATTTCTGTTTAGCTTGGAGCTGAATGTCATGACA
                                         tctgtcttct  CT-rich tract
     ataatatattattgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttattggtgaggaattaggacatttaactttgattttatgcctaatcataatatattattgtaagggcttattggtatgttgatctgtcttctgcagCACGCCAAATGAAGTGAAGGAAAGGATTTTGAAGGGAAGGATGGATTGAATTATAAGCCACCTGGGATTTCTGTTTAGCTTGGAGCTGAATGTCATGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA