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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcattatatgtattattgttcttttctgtgatctatctggaagatggatggcttttaacccaattgttttatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAGACCTATGTCATATTTGGTGAGGCGAAAATAGAGGACTTGAGCTCTCAGT

Basic information

species Glycine max
transcript GLYMA06G14250.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G14250.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G49470.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtcattatatgtattattgttcttttctgtgatctatctggaagatggatggcttttaacccaattgttttatgc-attagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAGACCTATGTCATATTTGGTGAGGCGAAAATAGAGGACTTGAGCTCTCAGT
|| |  | || | ||| || |   |   ||  |   | | ||||   |   |||  ||  | |  || |   || |||  || || |||| ||||| ||||| || ||||||||||| ||||| ||  |||| || |||||||| ||||| |||||||| || || ||||| |||||||||||| 
gtaaacctttctctgttttctcaataagtttagatttttttctgcgtgtgtgatt-ctaatgatacactacattaatgttatcagGTTCTCTTCTTTATCTCTAAGCCTGATGTCTTTAAGAGCCCGCATTCAGAAACCTATGTTATATTCGGTGAGGCCAAGATCGAGGATTTGAGCTCTCAGC

upper sequence: GLYMA06G14250.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0098g00830.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtcattatatgtattattgttcttttctgtgatctatctggaagatggatggcttttaacccaattgttttatgcat--tagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAGACCTATGTCATATTTGGTGAGGCGAAAATAGAGGACTTGAGCTCTCAGT
|| |    || | || |||  ||||||| |     ||  |  || |  ||| |||  | || |||   || |  |  || |   ||||  | || |||||||| || |||||||||||||||||||||||||| |||||||||||||||||||| |||||||| |||||||| |||||||||||| 
gtaaaattttgtctg-atttctgttcttgt-----attcacttgtatcatgaatg-ttctttaccagtttttcctgggcttggcagATATTATTTTTCATCTCAAAGCCTGATGTCTTCAAGAGTCCAAATTCAGAGACCTATGTCATATTTGGGGAGGCGAAGATAGAGGATTTGAGCTCTCAGC
















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|7693473|gb|AW761565.1|AW761565
EST:     GTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: GTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|6070688|gb|AW100075.1|AW100075
EST:     TCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|208036789|gb|GD833934.1|GD833934
EST:     TAAAACCTGTCACCGGTGTTAGTAAGGTCACAATCAAGAGAACAAAAA-T                         ATTCTTTTCTTCATCTCCAAACCTGAT
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGAT
EST: gi|193540925|gb|FK496073.1|FK496073
EST:     AAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCACCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: -AAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|21887816|gb|BQ741029.1|BQ741029
EST:     CACCAGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: CACC-GGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|207758914|gb|GD732209.1|GD732209
EST:     TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAAC-AAAAAT                         A-TCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|207690124|gb|GD671509.1|GD671509
EST:     TAAAACCTGTCACCGGTGTTAGTAAGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGAT
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGAT
EST: gi|26267872|gb|CA818935.1|CA818935
EST:     TAAAACCTGTCACCGGTGTTAGTACGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|21256107|gb|BQ452995.1|BQ452995
EST:     TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|33389132|gb|CA852339.1|CA852339
EST:     TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|254331636|gb|GR846053.1|GR846053
EST:     TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|58023736|gb|CX710477.1|CX710477
EST:     TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTNTTCTTCATCTCCAAACNTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|207823636|gb|GD796201.1|GD796201
EST:     TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|7589884|gb|AW705649.1|AW705649
EST:     AGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: AGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|193621812|gb|FK569160.1|FK569160
EST:     TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCC
genomic: TAAAACCTGTCACCGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtgatctatctggaagatggatggcttttaacccaattgttttatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAGACCTATGTCATATTTGGTGAGGCGAAAATAGAGGACTTGAGCTCTCAGT
                            ttttaac  putative branch site (score: 2)
                                       ttgtttt  putative PPT
                                     aattgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcattatatgtattattgttcttttctgtgatctatctggaagatggatggcttttaacccaattgttttatgcattagATTCTTTTCTTCATCTCCAAACCTGATGTCTTCAAGAGTCCAAATTCTGAGACCTATGTCATATTTGGTGAGGCGAAAATAGAGGACTTGAGCTCTCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA