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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgacgttttgtgtctttaagccttatttgggatgccattagagaagtgttttgcagctttagttgtactgatccatggacttgatgctatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAACCCAGTTACTTTGGATCATCTCAGTGTGAGAGGCAACAA

Basic information

species Glycine max
transcript GLYMA03G30880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 3'ss of exon 2
gtttgacgttttgtg-tctttaagccttatttgggatgccattagagaagtgttttgcagctttagttgtactgatccatggacttgatgctatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAACCCAGTTACTTTGGATCATCTCAGTGTGAGAGGCAACAA
 |  |  |   | |  || |   | | |   |   ||  | |     |     |         |   | | |  ||||            |||| |   ||||||||||||||| ||||| || ||  ||||||| || ||||| ||  ||||||||||||| || ||||| || ||||| ||||||||||| || |||||
-tcagcagagctattctcatgcggtcatgcctataatcacctccataagtgactccattatactccatatgcacatcctaacttccaggtctattttgtagGTGTTGATATCAGCATGAACACGCACCTGAAAACTGTGAAACTCACATTGAAAGGGAAAAATCCTGTTACCTTTGATCACCTCAGTGTGAGGGGAAACAA

upper sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0104g00160.t01 (Vitis vinifera), 3'ss of exon 4
gtttgacgttttgtgtctttaagccttatt--tgggatgccattagagaagtgtt--ttgcagctttagttg-tactgatccatggacttgatgctatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAACCCAGTTACTTTGGATCATCTCAGTGTGAGAGGCAACAA
     |     |   |   || ||  | ||  |||||   |||    ||| | |   |||        |  | | || ||   |||  |||      | | | |||||||||||| |||||||| ||||||||||| ||||| ||||| ||  |||| |||||||| ||||| ||| | |||||  | ||||| |||||||||||
-----atcaaatagataactaggcagttttaatgggaattcatgcatgaattctcagttgtgttgaaggcagattctaattagtggctttgcctgcttgttatagGTGTTGATATTAGTATGAACACACATTTGAAGACAGTGAAACTTACGTTGAAGGGGAAAAATCCAGTGACTCTAGATCACTTGAGTGTTAGAGGCAACAA

upper sequence: GLYMA03G30880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0015g01330.t01 (Vitis vinifera), 3'ss of exon 2
gtttgacgttttgtgtctttaagccttatttgggatgccattagagaagtgttttgcagctttagttgtactgatcc--atggacttgatgc-tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAACCCAGTTACTTTGGATCATCTCAGTGTGAGAGGCAACAA
    |    ||   ||   |||| |    ||  ||    |       ||  |     |   || |    |    | |  ||||  ||| |   ||| | | |||||| ||||| |||||||| ||||||||||| || || ||||| |||||||| |||||||| ||||| ||| ||||||| || |||||||| ||||||||
---agtaacttgaagtaggtaagtccatgttatgacaaaaactatttagaatcaaagatgattggagagatcattgctgatggtattgctttgtatgttatagGTGTGGATATTAGTATGAACACACATTTGAAGACTGTGAAACTGACTCTGAAGGGGAAAAATCCAGTGACTATGGATCACCTGAGTGTGAGGGGCAACAA

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|298174427|gb|HO014572.1|HO014572
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|9900352|gb|BE609320.1|BE609320
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|13480558|gb|BG509901.1|BG509901
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|31473802|gb|CD415830.1|CD415830
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|254323967|gb|GR836199.1|GR836199
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|12773904|gb|BG238831.1|BG238831
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|8827595|gb|BE211325.1|BE211325
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|4437132|gb|AI522997.1|AI522997
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|298198717|gb|HO042080.1|HO042080
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAGACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|27424994|gb|CA936514.1|CA936514
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|298193977|gb|HO040625.1|HO040625
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|15285034|gb|BI468925.1|BI468925
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|254334206|gb|GR849124.1|GR849124
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|7925936|gb|AW831962.1|AW831962
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|19269395|gb|BM885651.1|BM885651
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|254323968|gb|GR836200.1|GR836200
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|6846635|gb|AW348925.1|AW348925
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|15815172|gb|BI787447.1|BI787447
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|254334205|gb|GR849123.1|GR849123
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|298186306|gb|HO036939.1|HO036939
EST:     CGCTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|31468972|gb|CD411000.1|CD411000
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|298172347|gb|HO019387.1|HO019387
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTTATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|6482740|gb|AW201964.1|AW201964
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGCTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
EST: gi|31473716|gb|CD415744.1|CD415744
EST:     CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAG                         GTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA
genomic: CGTTTCAATCGAGCTCAAGAACGGAACAGTTGTTCATGGCACCATTACAGgttctcttct ... tatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtgttttgcagctttagttgtactgatccatggacttgatgctatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAACCCAGTTACTTTGGATCATCTCAGTGTGAGAGGCAACAA
               tttagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgacgttttgtgtctttaagccttatttgggatgccattagagaagtgttttgcagctttagttgtactgatccatggacttgatgctatatcacagGTGTTGATATCAGTATGAATACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAACCCAGTTACTTTGGATCATCTCAGTGTGAGAGGCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - ttttgtg
- - - - - - - - - - - - - - - - ggatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgcagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgatgc