Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG

Basic information

species Glycine max
transcript GLYMA10G35230.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 3'ss of exon 3
gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
                              | |       |  | ||| ||||| | |   ||  ||   | |  | |    | | |   | |    || ||       | |   |  | | |||||||   |   | |  | |||| |||||||| || || |||||||| |||||| | ||  || | || || |||||||| ||||||||||||||||||||||||||||| |||||
-----------------------------gtgaaacagacacttgattattttttacaggtttcctgtacagaggacac-accatttgattctccctataatatggcttattctattctgtttgtttta--ttaaatgaatttagGTGACTGTTGGTGCATCATTTTTGTCACAAACATTGGCGTTGGAGGATTCCACAACAGTAAAGTTTGAAATATGGGATACTGCTGGTCAGGAGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 3
gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
|| | ||  |||| || ||| || ||| ||| | ||  |||||| ||| ||     || | |  ||||          || |    || | | |||       | || |  ||   ||||| |  |  |       |||| | |||||||||| || || || ||||| || |||||| | ||| || | ||||| |||| ||| || ||||||||||||||||| ||||| ||||||||
gtgattac-tgtt-ttgagt-ctcttagtttcagttgataatgttattcttcaccttaga-tgcatga----------ttcttactttcagaagtt-------cgattgttttaaacttatttcctcaaa------taatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCAACAATAGTGAAATTTGAAATATGGGATACCGCTGGACAAGAGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 4
gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
                                      | || ||   | |||| ||    |  |      ||  | | | |  | | | | ||  |    ||||||    |        ||| || |  |     |  |   ||||||||||||| || |||||||| || |||||| | ||  || | || || |||| ||| ||||||||||| |||||||||||||| ||||||||
-------------------------------------gtgattta--ctgttttgatcagatcgacccatgaatgaaactttactttcggt-tgc-agcatttccat----tccccaacttatcttctcaa----atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 3
----gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttt-taatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
    |||||    |||||| || |  | || | || |   | | |     ||||     |  ||  | |      |   ||||||    | ||    | | | ||||       | | | ||| |    |  ||| || ||||   | |||||||||||||||| || || ||||| ||||| |||||  ||||||||||||| ||||| |||||||||||||||||||| || || || |||||
gtaagtaaagccttgttatctaattgtctt-tattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtat-acttatctgcc--actagatctcaagactactag-ctatgta---tcagGTAACTGTTGGAGCCTCGTTCTTGTCCCAAACTATAGCATTGCAAGACTCTACCACAGTGAAGTTTGAAATATGGGATACAGCAGGACAGGAGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtaaatatatgttatttagtac---ttttatttttattttttaatgta----attttttttaatatagtttatgacaaaaaaatattgtcgtc----ttgatatgttaa-----------ttattccatgg-aattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
              ||  ||||| |||| |  | |   |||| |||||   ||||| | ||    ||| | || ||  | ||||    | ||   || ||  | ||     |   |||  ||           ||||| ||||  |  | | |||| ||   ||   |||  |||  | |||| ||||| |||||||| || ||||| |||||||| ||  ||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||
gtaagaaatatacatagctatatattatgtgatgcacattttttttttcccttttattatattaaattctgttcaaccttgttttgtgccaatggatgttagcatcaatcctctcatgcaaaatacatggatgttatttcatgatagatttacttagattggttgatcttaataacttcagGTGACTGTAGGAGCTTCATTCTTGTCACAAACAATTGCCTTGCAAGATTCTACGACAGTTAAGTTTGAAATATGGGACACTGCTGGTCAAGAGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26700 (Selaginella moellendorffii), 3'ss of exon 3
gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG-----
                                                                                                || || | | |  ||| ||  |||| | |||| ||  | ||  |  | ||| |||||||| |||||||||||||||||||| |||||||| |||||||| |  ||||| |||||||| |||||||| || || || ||||||||     
----------------------------------------------------------------------------------------------gcaagtagtgcttttaat-gtgtttat-tatttt-gatatggtgctaca-gGTTACTGTTGGTGCTTCTTTTTTGTCGCAAACTATAGCTCTCCAAGACTCGAGCACAGTTAAGTTTGAGATATGGGACACCGCAGGACAAGAGAGATATG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26987 (Selaginella moellendorffii), 3'ss of exon 3
gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG-----
                                                                                               ||| || | | |  ||| ||  |||| | |||| ||  | ||  |  | ||| |||||||| |||||||||||||||||||| |||||||| |||||||| |  ||||| |||||||| |||||||| || || || ||||||||     
----------------------------------------------------------------------------------------------gtaagtagtgcttttaat-gtgtttat-tatttt-gatatggtgctaca-gGTTACTGTTGGTGCTTCTTTTTTGTCGCAAACTATAGCTCTCCAAGACTCGAGCACAGTTAAGTTTGAGATATGGGACACCGCAGGACAAGAGAGATATG

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|5605755|gb|AI899819.1|AI899819
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCANACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|193543327|gb|FK502506.1|FK502506
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|151394915|gb|EV264786.1|EV264786
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|192326781|gb|FK018908.1|FK018908
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|193724791|gb|FK658075.1|FK658075
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|15813084|gb|BI785359.1|BI785359
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|308098577|gb|HO760318.1|HO760318
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|298165609|gb|HO011658.1|HO011658
EST:     GCTGTATTGTTCTGCGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|298182667|gb|HO031402.1|HO031402
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|298183380|gb|HO028593.1|HO028593
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|7286166|gb|AW598653.1|AW598653
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|192296028|gb|FG989422.1|FG989422
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|298177777|gb|HO027330.1|HO027330
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|4277041|gb|AI431205.1|AI431205
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGCCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|151411846|gb|EV281657.1|EV281657
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCTAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|298185154|gb|HO030367.1|HO030367
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|15201204|gb|BI424748.1|BI424748
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
EST: gi|298174351|gb|HO017687.1|HO017687
EST:     GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG                         GTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT
genomic: GCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatat ... gtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG
  tgttaat  putative branch site (score: 3)
                        ttcttatatgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA