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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagaaagaaagggaacacacaacacaatttcttagattcgtagatgcacatctgttgtcaaaataatttttgatgtaatgcttgtttttcttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAATTGGAAATATGCCAGTGAAGTGTATGAGAAAGAGAGCTCTTAGTCTGAAG

Basic information

species Glycine max
transcript GLYMA06G14960.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G14960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g07950.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------taagaaagaaagggaacacacaacacaatttcttagattcgtagatgca-catctgttgtcaaaataatttttga---tgtaatgcttgtttttcttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAATTGGAAATATGCCAGTGAAGTGTATGAGAAAGAGAGCTCTTAGTCTGAAG
                          |    |    |   |     |  || ||||   |   ||  ||||   |   |||  |      | ||  |  ||   || |||| | ||   |  |  |||||||||| ||||| | | | ||||| || |||||||| ||||| ||||| || ||||||||||| |||||  ||||||||||||||||      | |||| |
gtgatttttccaggaatttaatattttggatatatgaaaaagtctgcttcagaattgagttc-tttatagacttagtttcttcttctgggaaaaactcggaatttgaaatgatcgtccctggtgatgcagTACAAAAATGTAAAAGCTGACTACCTGAAGAACATATGGAAGGTTATGAACTGGAAATATGCAAGTGAGTTGTATGAGAAAGAGAGT-----GCCTGAGG

upper sequence: GLYMA06G14960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g02990.t01 (Vitis vinifera), 3'ss of exon 5
taagaaagaaagggaacacacaacacaatttcttagattcgtagatgcacatctgttg-tcaaaataatttttgatgtaatgcttgtttttcttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAATTGGAAATATGCCAGTGAAGTGTATGAGAAAGAGAGCTCTTAGTCTGAAG
 ||      ||    | |     |   |  | |     || |   | | | | ||||  ||||  | ||||    |||     |  |||  | | |  |||||||||||||| || || || || || |||||| | |||||||| ||  | ||||||||||||||||||||||||||||||||| || |||   |   ||
caaattttcaattacataagattcgttacctatataggtcctgatttcccttgtgtttctcaatctgatttcatgtgtttcaatc-tttcccatgtgacagTACAAGAATGTGAGGCCGGATTACCTGAAGAACGTATGGAAAGTGATAGACTGGAAATATGCCAGTGAAGTGTATGAGAAAGAGTGCCCTTGAACAACAG
















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|254320557|gb|GR827006.1|GR827006
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|31306339|gb|CD391542.1|CD391542
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|213597364|gb|DB962098.1|DB962098
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACC
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACC
EST: gi|58018298|gb|CX705040.1|CX705040
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|16276939|gb|BI942120.1|BI942120
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|31309212|gb|CD394415.1|CD394415
EST:     CATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: CATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|193316645|gb|FK281913.1|FK281913
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATT
EST: gi|254343194|gb|GR859356.1|GR859356
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|209718433|gb|BW666245.1|BW666245
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|14999950|gb|BI320764.1|BI320764
EST:     TGGTTCCATTGATTGGTATTGATGGTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGG
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGG
EST: gi|213598309|gb|DB979901.1|DB979901
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|58021102|gb|CX707844.1|CX707844
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|151397983|gb|EV267856.1|EV267856
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|15589944|gb|BI674560.1|BI674560
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCA
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCA
EST: gi|31462032|gb|CD404060.1|CD404060
EST:     GTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: GTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|16278828|gb|BI943116.1|BI943116
EST:     TGGTTCCATTGCTTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTGAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|16278070|gb|BI942710.1|BI942710
EST:     TGGTTCCATTCCTTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTGAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|23734076|gb|BU765256.1|BU765256
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|31310328|gb|CD395531.1|CD395531
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|16276941|gb|BI942121.1|BI942121
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|208046523|gb|GD844291.1|GD844291
EST:     GGTTCCATTGCTTGGTATTGATGGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTGAAGAACATTTGGAAAGTTATTAAT
genomic: GGTTCCATTGATTGGTATTGATG-TTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|209718432|gb|BW666244.1|BW666244
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAA
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAA
EST: gi|58017804|gb|CX704546.1|CX704546
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
EST: gi|31470286|gb|CD412254.1|CD412254
EST:     TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAG                         TACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT
genomic: TGGTTCCATTGATTGGTATTGATGTTTGGGAGCATGCGTACTACTTACAGgtaaaatttt ... cttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacatctgttgtcaaaataatttttgatgtaatgcttgtttttcttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAATTGGAAATATGCCAGTGAAGTGTATGAGAAAGAGAGCTCTTAGTCTGAAG
                       ttttgat  putative branch site (score: 4)
                                    cttgtttttcttatt  putative PPT
             tcaaaataatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagaaagaaagggaacacacaacacaatttcttagattcgtagatgcacatctgttgtcaaaataatttttgatgtaatgcttgtttttcttattgcagTACAAGAATGTTAGACCAGACTATCTTAAGAACATTTGGAAAGTTATTAATTGGAAATATGCCAGTGAAGTGTATGAGAAAGAGAGCTCTTAGTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - aaagaaa
- - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - -gatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgta