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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttgtagaaactgaaaatgtctttttcaagctttatgaatcataataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG

Basic information

species Glycine max
transcript GLYMA13G27810.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 11
tatttgtagaaactgaaaatgtctttttcaagctttatgaat-cataataa-tgaacctatgctggatggc--atttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG
              | |  | ||||  |   |  || |||||   | |||| |   | | ||   | ||    || |  | | | |  ||       ||| |||||   |||  |  |||| ||||| |||||||| ||||| |||||||||||||| || ||||| || |||||||||||||||
--------------gtagttatcttgct---gtcttctgaatgtctgataactttccttgtgacagctgatcaatatttaacttgtattcaaacatcactacagGAGTGTGCCCTGCTGACCGATGGCAGATTTTCTGGAGGATCACATGGATTTGTTGTAGGCCACATTTGTCCTGAAGCACAG

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 11
tat-ttgtagaaactgaaaatgtcttt---ttcaagctttatgaatcataataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG
||  |||    |  || |  |||   |     | | | |  | | || | |  |  | |  |||   |||  | | | || ||  |   |  |    | | |||||    ||  |  |||| ||||| |||||||||||||| |||||||||||||| || ||||| ||||| ||||||||||||
taccttgatctagatgcacgtgtgcctggccactaccctggttattcttcactac-agctgatgt--gataacctcttaacca-gtgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCAGGAGGCTCACATGGATTTGTTGTCGGCCACATATGCCCTGAAGCACAG

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 11
tatttgtagaaactgaaaatgtctttttcaagctttatgaatcataataatgaacctatgctg-gatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG
|   |||       | || | || |  |        || | | ||  |     ||   || || |||  | | | || || ||   |  |    | | |||||    ||  |  |||| ||||| |||||||| ||||| |||||||||||||| || || || ||||| ||||||||||||
tgcatgtgtgcctggcaactatcctcctttcatcagattagttattcttcactacagttgatgtgataacctcttaacca-atgcccaatctccattacagGAGTGCGCCCTGCTGACAGATGGTAGATTTTCTGGAGGGTCACATGGATTTGTTGTCGGTCACATATGCCCTGAAGCACAG

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 11
----tatttgtagaaactgaaaatgtctttttcaagctttatgaatcataataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG
    |  |  |||| |      |||    |    | |  |  | | | |  |  | |    |||    |||  | ||   | || || |   || ||   |||||| ||||| || ||||||||||| || |||||||||||||||||||||| ||| |||||||| ||||||||||||||||| 
tatgttctcttagacatattttatgaacctgcttaacactgagtacctttgtt-tcatttgatgt--aatgttacttatggaattttattcctt-atgtggcagGATGTTGCTTTGTTGACTGATGGTAGGTTTTCAGGAGGTTCACATGGATATGTTGTTGGCCACATATGTCCTGAAGCACAT

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ18571 (Selaginella moellendorffii), 3'ss of exon 12
tatttgtagaaactgaaaatgtctttttcaagctttatgaatcataataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG
                                            |  ||| |  | | ||||   |  |      |  || |      ||  |  | |||||||| ||  |  | || ||||| ||||||||||||||||| ||||| ||||| ||||| || || ||||| ||||| |||
-----------------------------------------gtgtg-taaagttcgtttgctatgtttcgccatgaaaatctcactcctttct-ttccagGAAGTAGCTCTCCTCACGGATGGGAGATTTTCAGGAGGTTCTCATGGTTTTGTCGTTGGACACATTTGTCCAGAAGCCCAG

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ18570 (Selaginella moellendorffii), 3'ss of exon 11
tatttgtagaaactgaaaatgtctttttcaagctttatgaatcataataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG
                                            |  ||| |  | | | ||   |  |      |  || |       |     | |||||||| ||  |  | || ||||| ||||||||||||||||| ||||| ||||| ||||| || || ||||| ||||| |||
-----------------------------------------gtgtg-taaagttcgttttctatgtttcgccatgaaaatctcactccctttctttccagGAAGTAGCTCTCCTCACGGATGGGAGATTTTCAGGAGGTTCTCATGGTTTTGTCGTTGGACACATTTGTCCAGAAGCCCAG

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ36478 (Selaginella moellendorffii), 3'ss of exon 11
tatttgtagaaactgaaaatgtctttttcaagctttatgaatcataataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG
                                     ||  | |   |  |    ||||| |   || |||   || |  | |  ||||      | |||||||| ||  |  | || ||||| ||||||||||||||||| ||||| ||||| ||||| || || ||||| ||||| |||
------------------------------------gtgtgtaaagttcgttt-tctatgtt--ttgccatgataacctcactccctttct---ttccagGAAGTAGCTCTCCTCACGGATGGGAGATTTTCAGGAGGTTCTCATGGTTTTGTCGTTGGACACATTTGTCCAGAAGCCCAG

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|192320381|gb|FK013471.1|FK013471
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGGCTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|207777290|gb|GD750457.1|GD750457
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|193644416|gb|FK589882.1|FK589882
EST:     TGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: TGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|22927658|gb|BU544797.1|BU544797
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCNNNGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACNNGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|207747893|gb|GD720766.1|GD720766
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|208093555|gb|GD895702.1|GD895702
EST:     AGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: AGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|193353553|gb|FK322373.1|FK322373
EST:     AGATGTTAACACCTTAACTAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: AGATGTTAACACC--AAC-AAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|208239155|gb|GE037191.1|GE037191
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|193485361|gb|FK452473.1|FK452473
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|23734787|gb|BU765638.1|BU765638
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|193477699|gb|FK442288.1|FK442288
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|208054925|gb|GD852298.1|GD852298
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|208200339|gb|GE001323.1|GE001323
EST:     TTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: TTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|151400516|gb|EV270330.1|EV270330
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|193529516|gb|FK484833.1|FK484833
EST:     TGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: TGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|208287754|gb|GE081765.1|GE081765
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGA
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGA
EST: gi|16281629|gb|BI944586.1|BI944586
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTG
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTG
EST: gi|24136426|gb|BU926936.1|BU926936
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|207760482|gb|GD734505.1|GD734505
EST:     AGGTCTTGGAAAG                         GAAGTTTGTCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGAT
genomic: AGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAG-TTG-CATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGAT
EST: gi|193547225|gb|FK499594.1|FK499594
EST:     TGTTAACACCAAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: TGTTAACACC-AACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|151401192|gb|EV271006.1|EV271006
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|209715558|gb|BW682198.1|BW682198
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
EST: gi|208070506|gb|GD872611.1|GD872611
EST:     CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAG                         GAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT
genomic: CTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAAAGgtctgttttg ... gatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG
                                         ttttgat  putative branch site (score: 4)
                                       tcttttg  CT-rich tract
                                         ttttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttgtagaaactgaaaatgtctttttcaagctttatgaatcataataatgaacctatgctggatggcatttcaagcatattgtcttttgatactgcagGAAGTTGCATTATTGACTGATGGAAGATTTTCAGGAGGTTCACATGGATTTGTGGTTGGCCATATATGTCCTGAAGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - ttcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - cctatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatttc