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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgtttatcttctctttggcttgtattgtttataatataatttgaagtttttttctccccaatttatgatatcttcttactattactattttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT

Basic information

species Glycine max
transcript GLYMA13G19280.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------taatgtttatcttctc----tttggcttgtattgt--ttataatataatt---tgaagttt---ttttctccccaatttatgatatcttcttactattactattttggtc-agGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT
                                                                           | ||   ||| | ||     |  | |||   ||   | | || ||| ||   || | |     | ||     || ||     | |    || || ||  | | ||| |  ||||||| |||||||| || ||||||||||| || || || ||||| |||||||| ||||| || || |||||||| ||||||||| | |    || ||  |
gtaactcagctttgttttctcaaccagactccttgctctctagtactgttaatgttaaaactttcgagcatactaagtgccaatcctttcagatctgagtttgagctgcgctcagaacatatttgcatggaatgcaagtctttgttgcacttctctttttacatttgctgttcttctgttgctttagGTGACACATGCCGATTTCAAGAAGGCCAAAGAGAAGGTCATGTTCAAGAAGAAGGAAGGTGTACCGGAAGGGCTTTATATGTGAGACATCCACCACTCAT

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 5
------taatgtttatcttctctt-tggcttgta--ttgtttataatataatttgaagtttttttctccccaatttatgatatcttcttactattactattttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT-
       |  ||| | ||| | |  | || || |  |||  || ||  | |    || | |           | | ||||  |  | ||  ||||     ||  || |||| || ||||| ||||| ||||||||||| || || || ||||| |||||||||||||| ||||| || || || ||||||||| |  | |||  |     
attcaccagagttaaccttttgtaatagcctgcaacttgaatacaaggtcacagaaaatatcc---------actcatgaactgctatttttattttctgttgcgttagGTAACGCATGCAGACTTCAAGAAGGCCAAAGAAAAGGTTATGTTCAAGAAGAAAGAAGGCGTGCCGGAGGGCCTATATATGTGAGACTC-ATCAGCAGCGC

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 5
taatgtttatcttctctttggcttgtattgtttataatataatttgaagtttttttctccccaatttatgatatcttcttactattactattttggtc-agGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT
       ||     ||| |||||| |      | | || | ||   | |   | ||      | ||||   || | | |   |  |  | | |||||  ||||||| ||||  ||||| |||||||| ||||| || || ||||| |||||||||||||| || |||||||| || || |||||||  |    |  | | |
------gtaaggattctctggcttctcaccact-tgat-tcatcgaacgcaatctttgaataattttactttaacctttgtttggtcttctattggtttagGTGACGCATGTGGACTTCAAGAAGGCGAAGGAGAAGGTTATGTTCAAGAAGAAAGAAGGAGTTCCTGAAGGTCTTTACATGTGAATGATGCACAACGACT

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 5
---taatgtttatcttctctttggcttgtattgtttataatataatttgaa-gtttttttctccccaatttatgatatcttcttactattactattttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAA-ACTATCCTCTATT
     | ||| |     |     |  |  ||  ||  | || | | |                ||||||| |   |  ||  |||  | |||| |  |  ||||||||||||||  ||||| |||||||| ||||| || |||||||| |||||||||||||||||||| ||||| || || ||||||||| |||      ||| 
ggaagaagttgaatgcattacctgactacatgtttgctgattttagtcacctaggaccaggatcccaattaaatttgactggtta--aatactgtgct--tcagGTGACTCATGTAGACTTCAAGAAGGCAAAGGAGAAGGTGATGTTCAAGAAGAAAGAAGGGGTGCCAGAAGGACTTTACATGTGAAAACACTGCTACATAT-

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------taatgtttatcttctctttggcttgtattgtttataatataatttgaagtttttttctccccaatttatgatatcttcttactattact--attttggtc----agGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT
                                                                          || | | |   | | | ||      | | ||| ||||| | ||||  |  |||||||  | |  ||  ||  ||    |   | ||| |  || ||||||    |||||||||| | ||| || |||||||| || || |||||||||| ||||||||| || || |||||||| ||  |||| ||||  |  | |     |   |
gtgagactgttcgtattttgcatttcatgaatatgggcttcttgactagttgaaatcaggtgccagttatgcagtactttattattgcaccttcaaggttttagttgataatgtgattttga--ttttttcagcacggtt-gtgcaattaaatggatcttattggatgttggtcctgcagGTGACTCAAGTCGATTTCAAGAAGGCTAAAGAGAAAGTGATGTATAAGAAGAAGGAGGGCGTGCCTGAGGGTTTGTACATGTAGAGTATTCAGTACAGGT

upper sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------taatgtttatcttctctttg--gcttgtattgtt-tataatataa--tttgaagtttttttctccccaatttatga-tatcttcttactattactattt--tggt-cagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT-
                                                      |  | |||   | | || |  ||    || | | ||||||   |   ||  | ||   || |    | | | ||| ||  |  | ||| |   |  ||  ||   ||||||||||| || ||||| |||||||| ||||| ||||||||||  |||||||| ||||| || || || ||| | |||||||  || |||    || | | 
gtgagcttgccatttctttgtattcttttatatgtatttttaatgcgtctcgtcagaggttacacttttttagttgccctcatggctgtataattgcaggctttgaattggcttgttttgattctgtgactaagtattgactgtggattcttaatgccacagGTGACTCAAGCGGACTTCAAGAAGGCTAAGGACAAAGTGATGTACAAGAAGAAGGAAGGTGTACCCGAGGGGTTATATATGTAGAATACT-CAGTCAAGTG

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|16349378|gb|BI974973.1|BI974973
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|193729475|gb|FK664323.1|FK664323
EST:     GTCGAATGAAG                         GTGTACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAA
genomic: GTCGAATGAAGgtaagaaatc ... ttttggtcagGTG-ACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAA
EST: gi|193483348|gb|FK451443.1|FK451443
EST:     GTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: GTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|15337660|gb|BI498316.1|BI498316
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|27424837|gb|CA936357.1|CA936357
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|208049577|gb|GD849362.1|GD849362
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTG
EST: gi|207814023|gb|GD785916.1|GD785916
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCGTGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|209715036|gb|BW650887.1|BW650887
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|254325091|gb|GR834516.1|GR834516
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|21675930|gb|BQ628281.1|BQ628281
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|208328989|gb|GE126703.1|GE126703
EST:     AGAACGTCGAATGAAG                         GTGACTCATGCCGAC-TTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: AGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|193351248|gb|FK315004.1|FK315004
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|193431766|gb|FK393788.1|FK393788
EST:     AATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: AATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|58017107|gb|CX703849.1|CX703849
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|207751706|gb|GD723615.1|GD723615
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|193628955|gb|FK576405.1|FK576405
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|31459887|gb|CD401915.1|CD401915
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|33388030|gb|CA851237.1|CA851237
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|6846539|gb|AW348829.1|AW348829
EST:     CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|193559083|gb|FK515842.1|FK515842
EST:     AGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: AGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|7285842|gb|AW598329.1|AW598329
EST:     CTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
genomic: CTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG
EST: gi|31460408|gb|CD402376.1|CD402376
EST:     CCATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAG                         GTGACTCATGCCGACTTTAAGAAGGCCAAGGATCAAGTGATGTTTAAGAAG
genomic: CAATATGTACTGAAGCTGGTTTACTTGCTCTACGAGAACGTCGAATGAAGgtaagaaatc ... ttttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagtttttttctccccaatttatgatatcttcttactattactattttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT
                              ttcttac  putative branch site (score: 2)
                                          ctatttt  putative PPT
                                 ttactattactatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgtttatcttctctttggcttgtattgtttataatataatttgaagtttttttctccccaatttatgatatcttcttactattactattttggtcagGTGACTCATGCCGACTTTAAGAAGGCCAAGGATAAAGTGATGTTTAAGAAGAAAGAAGGGGTGCCTGAAGGGCTGTATATGTGAAAAACTATCCTCTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - tggcttg