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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtgatttaacgtcaaagatctttaagcatagtttctcaatgttcattaaagagacacagcttatattttttctgcctggtttctaatcatgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT

Basic information

species Glycine max
transcript GLYMA14G24270.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G24270.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G21720.1 (Arabidopsis thaliana), 3'ss of exon 5
cttgtgatttaacgtcaaagatctttaagcatagtttctcaatgttcattaaagagacacag-cttatattttttctgcctggttt--ctaatcatgaca--cagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT
   |  ||     ||  || |  | | ||| | |||   ||   | ||||  |       || ||||| | |       |||| ||  |  || | ||    |||||| | ||||||||||| ||||| || || |||||||| || |||||||| || ||||||||| ||||||| |||||||| ||||| ||  ||||
---ggcatgaggtgtttaatag-tctgagc-ttgttagccatactccattgtactactctagacttatgtatcgagactctggcttaacacatgaggattttcagGAAGCTGAGGAATTGTTCGAGACAATATCGCAAGCACTTCTCTCATCTGTTGACCGTGATTGTCTGAGTGGTTGGGGAGGGCATGTTTACATTGT

upper sequence: GLYMA14G24270.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g02260.t01 (Vitis vinifera), 3'ss of exon 5
cttgtgatttaacgtcaaagat---ctttaagcatagtt--tctcaatgttcattaaagagacacagcttatattttttctgcctggtttctaatcatgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT
 ||||| |   |      |      |||||  |||  ||  |  | ||||  |   ||  |   |||||   |||   |||   |    | |||  || |  |||||||| |||||||| ||||||| |||||| ||||||||||| ||||| ||||||||||| || |||||||| |||||||||||||||||||||||
attgtgctaagatacagcatgctccctttagtcatctttcgttcccatgtcaagctaatgggatcagct-gcattgactctttat----tttaactattattcagGAACCTGAGGAATTATTTGAGATCATCTCTCAAGCACTGCTCTCATCAGTAGATCGTGACTGCTTGAGTGGTTGGGGAGGACATGTCTATGTTGT
















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:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|192318542|gb|FK011366.1|FK011366
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|151405517|gb|EV275331.1|EV275331
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|7233908|gb|AW569250.1|AW569250
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|9819697|gb|BE555210.1|BE555210
EST:     ATCCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: AT-CTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|6914510|gb|AW396040.1|AW396040
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTGCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|16349184|gb|BI974779.1|BI974779
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|37995705|gb|CF807294.1|CF807294
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|192331116|gb|FK020336.1|FK020336
EST:     TATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|19346754|gb|BM891634.1|BM891634
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|298182182|gb|HO026357.1|HO026357
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|16104779|gb|BI892519.1|BI892519
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|151410578|gb|EV280393.1|EV280393
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|208277689|gb|GE078266.1|GE078266
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|298198899|gb|HO042262.1|HO042262
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|7233789|gb|AW569132.1|AW569132
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|23726885|gb|BU761446.1|BU761446
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|17519828|gb|BM188870.1|BM188870
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|26059647|gb|CA802561.1|CA802561
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|7926292|gb|AW832318.1|AW832318
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|16348147|gb|BI973742.1|BI973742
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|6914860|gb|AW396390.1|AW396390
EST:     GAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: GAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
EST: gi|26047837|gb|CA784494.1|CA784494
EST:     CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATG                         GAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA
genomic: CATCTGAGTCTCTGTATGGTGCTTGTGAGGCAATGTTTAAGCCTGACATGgtaggtcaca ... catgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaaagagacacagcttatattttttctgcctggtttctaatcatgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT
                                      ttctaat  putative branch site (score: 2)
                  ttatattttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtgatttaacgtcaaagatctttaagcatagtttctcaatgttcattaaagagacacagcttatattttttctgcctggtttctaatcatgacacagGAACCAGAGGAATTGTTTGAGACCATCTCCCAAGCACTGCTATCATCTGTAGATCGTGATTGTTTGAGTGGCTGGGGAGGACATGTCTATGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA