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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgcagttattgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat...

Basic information

species Glycine max
transcript GLYMA10G35230.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 5
TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgcagtta-ttgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat-----
||| || ||||| || || ||| | || || || | ||||||| |||| || || ||||| || |||||||| || ||||||||||| |||||||| ||||||   |  |    | || | || || | |  ||||  |  ||| ||  ||| |  ||  |  ||||      ||||| |    |    || ||| |   |     
TGCCTTGGCACCTCTTTACTACAGAGGAGCTGCTGCTGCAGTTGTTGTCTACGACATAACTAGTCCAGAATCATTTAGCAAAGCACAATACTGGGTGAAGgtatgctatcgccaaattatctgcttttctgatgtc--tggttgattgattactctttctatcttttac----tatgagtttgtattttttgcccgaaactgttct

upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 6
TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgcagttat--tgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat
||| || || || || || ||| | || || || | |||| || |||| |||||||||||||| || ||||| || |||||||||||||| ||||| |||||| | |   ||  |   | ||   ||||   || | ||   | ||||| |      |    | | | ||    |     |     | |  ||   | | | 
TGCCTTGGCGCCACTTTACTACAGAGGAGCTGCTGCTGCAATTGTTGTCTATGATATAACAAGTCCGGAATCATTTAGCAAAGCACAGTATTGGGTAAAGgtaaagtataagcaaccctctactcttctgagttcttatccttggttttctccccattccctattatcgacctgtgcatcttcttga-agctctgatgtaa-

upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 5
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 5
TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgcagtta--ttgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat
|||  | ||||| ||||| |||||||| || | |||||| |||||||| ||||||||||||||||| ||||| ||||  ||||||||||| ||||||||||||  ||| |||     |   | ||||| || | ||   |  || |    || ||      |  ||  ||   ||||   || ||           ||    
TGCTCTTGCACCACTATACTACCGTGGAGCTGGAGTTGCTGTTATTGTGTATGATATAACAAGCCCTGAATCGTTCAAGAAAGCACAGTATTGGGTTAAGgtatgttttcagggggttcaaaaggttccatttcgttcatgtttctaggattcgt-gcaatagcttccgagctatatctttaccaggactgaaaattagag-

upper sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 5
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 5
TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagattt-----gcagttattgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat
|||| | ||||| || || || || ||||| |||||||||||| | || ||||||||||||||||||||||| |||| |||||||||||| ||||||||||||  |||     | ||  | || |    | | ||||    ||||||  ||  ||| ||||||  | || |   || |      |   |   ||| |  | |   
TGCGCTGGCACCACTTTACTATCGAGGTGCTGCAGTTGCAGTTGTAGTGTATGATATAACAAGCCCAGAATCATTCAACAAAGCACAGTATTGGGTTAAGgtatctttttttagtaggaagtgcaatagtatttatttctgtttctttcttgcttaattatttctatttct--ttgcttgcttcatttatttatttcttttt---

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:     ATGATATAACAAGCCCAGAATCTTTCAGCANAGCACAGTACTGGGGTAAG                         GAGCTACANAAACATGGAAGCCCTGATATAGTGATGGCACTTGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|208204745|gb|GE006542.1|GE006542
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAA-CATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|7286166|gb|AW598653.1|AW598653
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|298182667|gb|HO031402.1|HO031402
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT
EST: gi|15201204|gb|BI424748.1|BI424748
EST:     ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAG                         GAGCTACAAAAACATGGAAGCCCTGATATAATGATGGCACTGGTCGGTAAT
genomic: ATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgc ... aattttttagGAGCTACAAAAACATGGAAGCCCTGATATAGTGATGGCACTGGTCGGTAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGTTAGCACCGCTATATTACCGTGGTGCAGCAGTTGCAGTTATTGTTTATGATATAACAAGCCCAGAATCTTTCAGCAAAGCACAGTACTGGGTTAAGgtagatttgcagttattgtatggttctatattgtcatttcttgttttgttagttatttgaaattttgaatgatatgaataacaaacaattcccctatcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcccct