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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttggattactcttacctttagtgattattccattaccataagctagagagtatacagacattatatattttaattttcattcagttattcttcatgatgtctgcattctactttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC

Basic information

species Glycine max
transcript GLYMA03G07890.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 7
gtatgttggattactcttacctttagtgattattccattaccataagctagagagtatacagacattatatattttaattttcattcagttattcttcatgatgtctgcattctactttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC
                 || |||   ||||  |||||||    | | ||      ||| | |         |    ||     ||||| ||| ||||| |||| | || |            ||||||| || || || ||||| || ||||| ||||||||||| |||||  |||| ||||||||||| |  |||||||||||  |||  |||||||| || ||
----------------gtatcttc--tgatc-ttccattcttgtcaact------tatgctgctgagccgaac---aa-----attcaattaatcttc-tgatttatgtac-----------cagGTCTGCTTGGGACTGCTGCTTTCGCATTCTTCTGCTTCTATCTTCTTATTGCAGTGATTGCTGGGGAGATGATGCTTGGATTGAAGCTAGTTTTTATCAC

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G08930.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgttggattactcttacctttagtgattattccattaccataagctagagagtatacagacattatatattttaattttcattcagttattcttcatgatgtctgcattctactttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC
                             | | | |||     |   || |  |   |  | |   | | |  |||  || | | | |      || |||| ||  | | |       ||  |||||||| | || || ||||| ||||| || ||||| ||||||||||| |||||||| || ||||| || |||||||| ||  |||  || || ||||||||
----------------------------gtaagttcatacttttgtccttgttatcctgtataaggtttcttctttgtttctaactga------ctccatgctgg-tacgtgtggaaatctccagGTCTTTTAGGCACTGCTGCCTTTGCTTTCTTCTGTTTCTACCTTCTACTTGCTGTTATCGCTGGGGCAATGATGCTGGGTTTGAAGCTGGTCTTCATTAC

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgttggattactcttacctttagtgattattccattaccataagctagagagtatac---agacattatatattttaattttcattcagttat-tcttcatgatgtctgcattctact-ttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC
                             | | | ||||  | | | || |  |   |||   | || || |   ||||   | | |    | | | | |||||        |||| |  | ||||  ||||||||| || |||||||| ||||| || ||||| ||||| || || |||||||| |||||||| || |||||||||||  |||  || || ||||||||
----------------------------gtaacttcattttc-tgatcttgttatgctactctataccttgttccttttgtgtctgacctggctctgtgttcatacatgtgacattttcttgttcactagGTCTTCTTGGCACAGCTGCCTTTGCTTTCTTCTGTTTCTATCTCCTACTTGCTGTTATTGCTGGGGCAATGATGCTTGGTTTGAAGCTGGTCTTCATTAC

upper sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 9
gtatgttggattactcttacctttagtgattattccattaccataagctagagagtatacagacattatatattttaattttcattcagttattct-tcatgatgtctgcattctactt--tcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC
                                    | | | |||   |   |      | |  ||| ||| |  |    |||| |   | ||  | |  |||  | |   || |||||  || ||||||||  ||||||| || ||||||||||| ||||||||||||||||| ||||| |||||||| || || ||||||||||| || ||| |||||||||||||
----------------------------------gtactgctatagatttttgctgtctctgttattttatttcct----ttcactagatgatcttattctgagatgtatcttgtacttcttcgtcagGTCTCTTGGGTACTGCAGCATTTGCATTCTTCTGCTTCTACCTTCTGCTTGCGGTGATTGCAGGGGCAATGATGCTTGGACTTAGATTAGTTTTCATTAC

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|18730359|gb|BM525833.1|BM525833
EST:     TCTTTCTCCTTTCTTGAATGAAGTTTTCATCAAGTTGGATGATATCTGGG                         GTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTG
genomic: TCTTTCTCCTTTCTTGAATGAAGTTTTCATCAAGTTGGATGATATCTGGGgtatgttgga ... ctttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTG
EST: gi|58025422|gb|CX712163.1|CX712163
EST:     TCTTTCTCCTTTCTTGAATGAAGTTTTCATCAAGTTGGATGATATCTGGG                         GTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTG
genomic: TCTTTCTCCTTTCTTGAATGAAGTTTTCATCAAGTTGGATGATATCTGGGgtatgttgga ... ctttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttaattttcattcagttattcttcatgatgtctgcattctactttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC
  ttttaat  putative branch site (score: 3)
                                        ttctactttc  putative PPT
     taattttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttggattactcttacctttagtgattattccattaccataagctagagagtatacagacattatatattttaattttcattcagttattcttcatgatgtctgcattctactttcatcagGTCTTCTGGGTACAGCTGCATTTGCATTTTTCTGCTTCTACCTTCTCCTTGCTGTGATTGCTGGAGCCATGATGCTTGGGCTGAGACTAGTTTTCATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA