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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttcttatccgttatttatttatttatttttaggaaaatttcacatctgtttatgttgtttatttgtttttttttttaaattgtttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTGCTATCCACTCTCATGTTGTGAGGGTTCGATCCCGCACCGACAGGAGGAA

Basic information

species Glycine max
transcript GLYMA14G38950.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G38950.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G56340.1 (Arabidopsis thaliana), 3'ss of exon 3
------------gtaattttcttatccgttatttatttatttatttttaggaaaatttcacatctgtttatgttgtttatttgtttttttttttaaattgtttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTGCTATCCACTCTCATGTTGTGAGGGTTCGATCCCGCACCGACAGGAGGAA
              | | || |||| | || || |||  | |||||    | || |||    |  |  |     || || ||| |||| | |||  ||||   ||  | ||  || || || ||||| || || |  |||| |||||||||||| || ||||||||||| ||||| |||||||| || |||||||||||| || | ||   
gtatgtgttgatagattcttgttatgcattgttaatt-gtgtattt----ggaattttgttttgagacttcagagtgtaattggttttgtatttgtattgc--attggtagGTTACACTCTCCCAAAGCTTTACGCTAAGACGCAGTACTGTGTCTCGTGTGCTATCCATTCTCACGTTGTGAGAGTCCGATCCCGCACCAACCGTAGAGT

upper sequence: GLYMA14G38950.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G40590.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtaattttcttatccgttatt-tatttattt-atttttaggaaaatttcacatc------------tgtttatgttgtt--tatttgtttttttttttaaattgtttatgtg-----cagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTGCTATCCACTCTCATGTTGTGAGGGTTCGATCCCGCACCGACAGGAGGAA
   | ||||  ||   |  | || | ||| ||| |  |||   | ||||  ||||             | ||||   | ||   ||| | |||     || | |   | ||||      ||| ||| ||| | || || || ||||  |||| ||| |||||||| |||||||||||||||||||| || || || || || ||||||||| || | |||  
gtatcatttcattcctctcttttatgtttctttgacctttgttataattctacattataaagtttggatttttagactattggcattagatttccagcttgattgaatcatgtaattgacagGATACACATTGCCGAAGCTATATGCAAAGACGCAATACTGTGTCTCCTGTGCTATCCACTCTCACGTCGTTAGAGTCCGTTCCCGCACCAACCGTAGGGT

upper sequence: GLYMA14G38950.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G40510.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------gta-attttcttatccg--ttatttatttatttatttttaggaaa-----atttcacatctgtttatgttg---tttatttgttttt-----ttttttaaattgtttatgtg-cagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTGCTATCCACTCTCATGTTGTGAGGGTTCGATCCCGCACCGACAGGAGGAA
                                                  || ||| |    |  |  || ||    ||||  | || || ||      ||||  |  || ||    |||   |||| |    | |     ||  || |||  | ||  || ||| ||| ||| | || || || ||||  |||| ||| |||||||| ||||||||||||||||||||||| || || || || ||||||||| || | |||  
gtatcatttcattcctctcttttatgtttctttgacctttgttataattctacattataaagtttggatttttagactattggtattgagaaagtttggatttttcgactattggcattgaagtttactgagatctgtaacttgattgaatcatgtaattgacagGATACACATTGCCGAAGCTATATGCAAAGACGCAATACTGTGTCTCCTGTGCTATCCACTCTCATGTCGTTAGAGTCCGTTCCCGCACCAACCGCAGGGT

upper sequence: GLYMA14G38950.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 4
gtaattttcttatccgttatt-tatttatttatttttaggaaaatttcacatctgtttatgttgtttatttgtttttttttttaaattgtttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTGCTATCCACTCTCATGTTGTGAGGGTTCGATCCCGCACCGACAGGAGGAA
               || |||  | ||  |  |||||  |  |||||        | | |||| ||||| || |||      ||| |    | |||| ||  ||||| ||||| || || ||||  ||||||||||||||||| || ||||| || ||||| ||||||||||||||||| || ||||| || ||||||||
---------------gtaattacacttcctctttttttcggtaatttgt------tctgtgttttttatctgatttgggggctaatt---ctctgtgtagCTTATACTCTTCCCAAGCTGTATGCAAAGATGCAGTACTGTGTGTCTTGTGCAATTCACTCCCATGTTGTGAGGGTTCGTTCTCGCACTGATAGGAGGAA

upper sequence: GLYMA14G38950.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 3'ss of exon 3
gtaattttcttatccgttatttatttatttatttttaggaaaatttcacatctgtttatgttgtttatttgtttttttttttaaattgtttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTGCTATCCACTCTCATGTTGTGAGGGTTCGATCCCGCACCGACAGGAGGAA
||||||  ||| |   | | |  ||| | | || ||         |    | || | ||| || |    ||  ||| | |||   || |   |||| ||  ||||| || || ||  | ||||  |||||||||||||||||||| ||||| || || || |||||||| |||||||| |||||||| ||||| |||||
gtaatt--cttctttatcaatactttctatcttctt--------cttctttatggtgatgatgatccactgagtttgtattt---ttctacttgtgaagCTTATACTCTCCCCAAGTTGTATGCCAAGATGCAGTACTGTGTTTCTTGTGCAATTCATTCGCATGTTGTTAGGGTTCGTTCCCGCACTGACAGAAGGAA

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|298185816|gb|HO030977.1|HO030977
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC                         AATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAACgtaattttct ... ttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|7145743|gb|AW507665.1|AW507665
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC                         AATATACACTTNCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAACgtaattttct ... ttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|193356347|gb|FK323060.1|FK323060
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC                         AATATACACTTCCAAAACTCTATGTGAAGA
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAACgtaattttct ... ttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGA
EST: gi|193424383|gb|FK391660.1|FK391660
EST:     GTGTCTATGAAC                         AATATACACTTCCAAAACTACTATGTGAAGATGCAGTACTGTGTTTCCTGT
genomic: GTGTCTATGAACgtaattttct ... ttatgtgcagAATATACACTTCCAAAACT-CTATGTGAAGATGCAGTACTGTGTTTCCTGT
EST: gi|20449728|gb|BQ253860.1|BQ253860
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC                         AATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAACgtaattttct ... ttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|193661392|gb|FK601716.1|FK601716
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC                         AATATACACTTCCAAAACTCTATGTGAAGATGCAGTA
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAACgtaattttct ... ttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTA
EST: gi|193344296|gb|FK312826.1|FK312826
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC                         AATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAACgtaattttct ... ttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
EST: gi|298193611|gb|HO040259.1|HO040259
EST:     TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAAC                         AATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG
genomic: TGTTGAACAGGCTGCAGTCAGAGATGTGCAGGAAGCTTGTGTCTATGAACgtaattttct ... ttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacatctgtttatgttgtttatttgtttttttttttaaattgtttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTGCTATCCACTCTCATGTTGTGAGGGTTCGATCCCGCACCGACAGGAGGAA
          tttatgttgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttcttatccgttatttatttatttatttttaggaaaatttcacatctgtttatgttgtttatttgtttttttttttaaattgtttatgtgcagAATATACACTTCCAAAACTCTATGTGAAGATGCAGTACTGTGTTTCCTGTGCTATCCACTCTCATGTTGTGAGGGTTCGATCCCGCACCGACAGGAGGAA

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