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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcacttagcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG

Basic information

species Glycine max
transcript GLYMA08G37270.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 6
acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcacttagcatcttcattatctgcatctaatattgctgctactacta------tgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG
  |   |||  |   |  ||| | | | ||||    || | |   ||| | ||| | |   ||||  ||  |||    || |  | | ||| ||       ||||||||||||| || ||||| || ||||| |||||||| |||||||||||||| ||  ||||| ||||||| || || |  || || ||||| |||
tgagtttcttccccctcaattcttagttatgt--tcagatat---aatgctcttggtactctcatcctcc-catggcttagttgttcaacttcttgatggttgcagACTGATACTAAGAAGATTTCAGCAGTTTCGATATTCTTTGAGACAATGCCCTACAGATTGGATGAAAGCACTGGCTTGATTGATTATGATCAG

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 6
----acaagctc-tatcagttgtattttaattcat-gtaacaagctctctcaattcacttagcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG
     |||     |  || ||     | ||||| | ||||||  |       || | ||    |     ||        || ||  ||    |||||  | |||||||||| || || ||||||||||||   || |||||||||||||||||||| ||  ||||| ||||||| || ||||  || || || || |||
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcctatagc-----tcaaaggttctacctactgtt-tgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAG

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G135283_T01 (Zea mays), 3'ss of exon 6
----acaagctc-tatcagttgtattttaattcat-gtaacaagctctctcaattcacttagcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG-------
     |||     |  || ||     | ||||| | ||||||  |       || | ||    |     ||        || ||  ||    |||||  | |||||||||| || || ||||||||||||   || |||||||||||||||||||| ||  ||||| ||||||| || ||||  || || || || |||       
atctgcaaatgaatgacattttcccataaattcttagtaacattcagatatgatgctctagatactcctatagc-----tcaaaggttctacctactgtt-tgcagACTGACACTAAGAAGATATCTGCAACTTCAATATTTTTTGAGACAATGCCTTACAGATTGGATGAAAGCACTGGATTGATTGATTACGATCAGGTCATTT

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 3'ss of exon 6
acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcac-ttagcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG-------
      ||||  | |||    |   | | |||     |   | | | ||  | ||   || | |         | ||  |  |       ||| | ||||||| || ||||| || ||||||||||| || |||||||||||||||||||||||| |||||||||| || || || ||||| ||||||||||||       
-aggtttctaatatttgatgatctctccttgtttgtggtattattactttgccttcttatgtgctagggagtaacctcctcatttcttcgctattgtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAGGTAACTT

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 6
acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcactta---gcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG
      ||||  | |||    |   | | |||     |   | | | ||  | |       |  |    |     | ||  |  |       ||| | ||||||| || ||||| || ||||||||||| || |||||||||||||||||||||||| |||||||||| || || || ||||| ||||||||||||
---gtttctaatatttgatgatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttcttcgctattgtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcactta---gcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG
      ||||  | |||    |   | | |||     |   | | | ||  | |       |  |    |     | ||  |  |     | ||| | |||||||||| ||||| || ||||||||||| || |||||||||||||||||||||||| |||||||||| || || || ||||| ||||||||||||
---gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgctattgtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

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|151402224|gb|EV272037.1|EV272037
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209699627|gb|BW655719.1|BW655719
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209715301|gb|BW654188.1|BW654188
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209699197|gb|BW656186.1|BW656186
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|120529377|gb|EH257511.1|EH257511
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|213588396|gb|DB967882.1|DB967882
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209704314|gb|BW683546.1|BW683546
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATANNNNNNNGAGACA-TGCC
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTT-GAGACAATGCC
EST: gi|120530707|gb|EH258840.1|EH258840
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|120533051|gb|EH261184.1|EH261184
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209724195|gb|BW659729.1|BW659729
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209715019|gb|BW650870.1|BW650870
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209709691|gb|BW668227.1|BW668227
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|14205774|gb|BG839452.1|BG839452
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209700117|gb|BW652975.1|BW652975
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCATGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209708166|gb|BW673829.1|BW673829
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATA
EST: gi|209715940|gb|BW650957.1|BW650957
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|213599231|gb|DB962282.1|DB962282
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGAC
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGAC
EST: gi|213597587|gb|DB962553.1|DB962553
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAG
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAG
EST: gi|213617635|gb|DB969347.1|DB969347
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAA
EST: gi|209727383|gb|BW651931.1|BW651931
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209725631|gb|BW663120.1|BW663120
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGANCA-TGCC
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGA-CAATGCC
EST: gi|213587994|gb|DB957453.1|DB957453
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|120533233|gb|EH261366.1|EH261366
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|209710568|gb|BW676520.1|BW676520
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA
EST: gi|22539787|gb|BU089630.1|BU089630
EST:     TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAG                         ACTGATACCAAAAAGATATCTGCAGTCTCGATATTGTTTGAGACAATGCCA
genomic: TCATGGCACTTGATCTTCCTCATGGTGGCCATCTTTCTCACGGATATCAGgtactttgaa ... tactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcacttagcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG
                           atctaat  putative branch site (score: 3)
                           atctaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaagctctatcagttgtattttaattcatgtaacaagctctctcaattcacttagcatcttcattatctgcatctaatattgctgctactactatgcagACTGATACCAAAAAGATATCTGCAGTCTCGATATTTTTTGAGACAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG

- - - - - - - - - - - - - -catgtaa
- - - - - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctgc