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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttgtttattcttgttctctcttcattattttattgtcttccatttcactatcctgatgatgaaaaattaatatatagttactattttcacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCATATAGACTGAACGAAAACACGGGACACATTGACTATGATCAG

Basic information

species Glycine max
transcript GLYMA09G33480.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 3'ss of exon 6
---tctttgtttattcttgttctctcttcattattttattgtcttccatttcactatcctgatgatgaaaaattaatatatagttactattttcacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCATATAGACTGAACGAAAACACGGGACACATTGACTATGATCAG-------
   | | |  |  ||  || |||||| |  |  || |  | |  |   |||  ||       || |    | | |     |  || || |    |   ||||||| |||||||| ||  |||||||||| ||  |||||||||||||||||||||||||| |||| || | ||| ||  ||||||||||||| |||       
aggtttctaatatttgatgatctctccttgt--ttgtggtattattactttgccttcttatgtgctagggagtaacctcctcatttct-tcgctattgtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAGGTAACTT

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 6
-tctttgtttattcttgttctctcttcatt----attttattgtcttccatttcactatcctgatgatgaaaaattaat-atatagttactattttcacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCATATAGACTGAACGAAAACACGGGACACATTGACTATGATCAG
 | | |  |  ||  || |||||| |  ||     | |||||   || | ||    | | ||   ||    ||  |  | || |  |  |||||       ||||||| |||||||| ||  |||||||||| ||  |||||||||||||||||||||||||| |||| || | ||| ||  ||||||||||||| |||
gtttctaatatttgatgatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttcttcgctatt------gtgcagACCGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 6
-tctttgtttattcttgttctctcttcatt----attttattgtcttccatttcactatcctgatgatgaaaaattaat-atatagttactattttcacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCATATAGACTGAACGAAAACACGGGACACATTGACTATGATCAG
 | | |  |  ||   | |||||| |  ||     | |||||   || | ||    | | ||   ||    ||  |  | || |  || |||||       |||||||||||||||| ||  |||||||||| ||  |||||||||||||||||||||||||| |||| || | ||| ||  ||||||||||||| |||
gtttctaatatttgaggatctctccttgtttgtggtattattactttgccttcttatgtgctagggacagtaacctcctcatttctttgctatt------gtgcagACTGACACCAAGAAAATATCTGCAGTGTCTATATTTTTTGAGACAATGCCATATAGATTGAATGAGAGCACTGGCTACATTGACTATGACCAG

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|207755695|gb|GD728946.1|GD728946
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|207692648|gb|GD674873.1|GD674873
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACCCCAATAAGGTATC
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATC
EST: gi|193419865|gb|FK381933.1|FK381933
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|193438324|gb|FK400033.1|FK400033
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGG
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGG
EST: gi|193325818|gb|FK290257.1|FK290257
EST:     ACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCGATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: ACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|193444846|gb|FK405272.1|FK405272
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTT-GAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|193455615|gb|FK418780.1|FK418780
EST:     ACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: ACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|207707628|gb|GD689086.1|GD689086
EST:     TACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|208174031|gb|GD967292.1|GD967292
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|207683188|gb|GD665909.1|GD665909
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCT
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCT
EST: gi|207773709|gb|GD745743.1|GD745743
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|208046332|gb|GD847250.1|GD847250
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGAC
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGAC
EST: gi|208093400|gb|GD895239.1|GD895239
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCG
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|208160227|gb|GD953483.1|GD953483
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|208025377|gb|GD823425.1|GD823425
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACCCCAATAAGGTATC
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATC
EST: gi|193422500|gb|FK387593.1|FK387593
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGTAGTACAATGC
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTG-AG-ACAATGC
EST: gi|193494239|gb|FK459263.1|FK459263
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|193551975|gb|FK506562.1|FK506562
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|207714334|gb|GD695855.1|GD695855
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|193543131|gb|FK503682.1|FK503682
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|208083643|gb|GD884027.1|GD884027
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|193313395|gb|FK282024.1|FK282024
EST:     TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|208038129|gb|GD837025.1|GD837025
EST:     ATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: ATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|208220568|gb|GE017144.1|GE017144
EST:     TCATGG-ACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: TCATGGGACTTGATCTACCACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
EST: gi|193316056|gb|FK281422.1|FK281422
EST:     GACTTGATCTTACCTACATGGAGGGCATCTTTCTCATGGATACCAG                         ACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA
genomic: GACTTGATC-TACC-ACATGGAGGGCATCTTTCTCATGGATACCAGgtattatcaa ... cacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcactatcctgatgatgaaaaattaatatatagttactattttcacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCATATAGACTGAACGAAAACACGGGACACATTGACTATGATCAG
                      aattaat  putative branch site (score: 3)
                                      ctattttc  putative PPT
                atgaaaaattaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttgtttattcttgttctctcttcattattttattgtcttccatttcactatcctgatgatgaaaaattaatatatagttactattttcacaatgcagACTGACACCAATAAGGTATCTGCAGTCTCCTTATTTTTTGAGACAATGCCATATAGACTGAACGAAAACACGGGACACATTGACTATGATCAG

- - - - - - cttgttc
- - - - - - - - - - ctcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattaa