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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ17802
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag--------------------------------------------
||||||| ||||||||||| || || || || || |||||||| ||||||||||||||||| |||||||||||||||||||||||||| || |||||||||| ||  |  ||||  | ||| |  |  |  | ||||  ||||   | ||      |                                              
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgt-cagcca-tggacgc-ggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgc--tcgacactagggtatcgat--ctaactcttggtttcg------tgttgcag----------------------------------------------------------------------------------------------------------
||||||| ||||||||||| || || || || || ||||| |||||||||||||||||||| |||||||||||||||||||||||||| || || |||||||||  |   |  |||  | | |||     | ||     |||  | ||||   ||      | | ||||                                                                                                          
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag----------------------------------------------------------------------------------------------------------------------------------------------
||||||| ||||||| |||||| || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || |||||||||    ||  || | |  | |        |||| |   |           |   |                                                                                                                                                
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcc-cgtcccctcccctcccccctcccccgatttcgttaccccacaaacgccccccctggagtccgttaatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G022206_T02 (Zea mays), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtagga----------atgtagccgctcgacactagggt--atcgatctaactcttggtttcgtgttgcag-----------------------------------------------------------------------------------------------------------
||||||| ||||||| |||||| || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||             |   |||| | |  | |  | ||   |  |||   ||| || | | | |||  |                                                                                                            
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtacctcatccatcccacagagccccccaccccccgagtccgttaatcccgctcctgttctagggtttgattgacaggttccggatcttgggggggtgagaaacgggttctcatctattcctttccattttcactcgtgtttgttgtgctgatgagagaggttcgtttgattttgcag

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaact--cttggtttcgtgttgcag------------------------------------------------------------------
||||||| |||||||||||  | || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||   ||   |||||      ||  | | |     || ||  | |       || ||  |                                                                  
TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgta---atcaggccgcctatttctgtgatgttaggttagctagcctaaggatctgatgaggtgcgaggctgcaatacttacggtgctgactgtgcttttgctattgtcgtttgttgcgattctgcag

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G120674_T01 (Zea mays), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctc----gacactagggta-tcgatctaac--tcttg-gtttcgtgttgcag------------------------------------------------------------------
||||||| |||||||||||||| || || || || ||||| || ||||||||||||||| | |||||||| ||||||||||||||||| || || ||||||||  |      |   |     ||   |||| ||      ||||   ||| | |   ||||  || |                                                                  
TGATGCGGGACTTCAAGCGCCTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGTACGACAACAATATCATGCTCTGGAACGCCGTCATATTCGGgtatcagcccgcctatttctgtgatgttaggttagctagcctaaggatctagtgaggcgtgaggccgcgatacttttggtgggttttaatgctgactgtgctttttctcttggtgtttgttgcgattctgcag

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag--------------------------------------------------------------------------------------------
| ||| |||| |||||| | || ||||| || ||||| || |||||||| ||||| || ||||| |||||||||||||| ||||| || || || || ||||  |  || |          |  | | ||    | |    |||  ||   |  |  ||                                                                                            
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagc-tgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G10640.3 (Glycine max), 5'ss of exon 2
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag------------------------------------------
| ||| |||| |||||| | || ||||| || ||||| || |||||||| ||||| || ||||| |||||||||||||| ||||| || || || || ||||  |  || |          |  | | ||    | |    |||  ||   |  |  ||                                          
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagc-tgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgta

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgttgcag------------------------------------------
||||||| |||||||||||| | ||||| |||||||| || || ||||||||||| |||||||||||||| |||||||| ||||| || ||||| ||||||||   | ||  |  |  |    | |  | | | || |     |    ||||| ||| |                                          
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgcctccctggt-ttcgttttttgttcaattgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt

upper sequence: EFJ17802 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcgacactagggtatcgatctaactcttggtttcgtgt-tgcag----------------------------------------
||||||| |||||||||||||| || || |||||||| || || ||||||||||| ||||||||||||||||||||| | ||||| || || || ||||||||   |     |  | |||   | |     |   || | |  ||      ||  |||                                          
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaactcctccccgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatggcggtgtcggttt

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|169066636|gb|FE473572.1|FE473572
EST:     GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGG                         GCCGGATGACACTCCCTGGGATGGAG
genomic: GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG
EST: gi|169115252|gb|FE515642.1|FE515642
EST:     GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGG                         GCCGGATGACACTCCCTGGGATGGAG
genomic: GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG
EST: gi|169071067|gb|FE480695.1|FE480695
EST:     GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGG                         GCCGGATGACACTCCCTGGGATGGAG
genomic: GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG
EST: gi|169071014|gb|FE480694.1|FE480694
EST:     GGCGCGCCGCAGGACAACAACATCATGCTTTGGAACGCGGTGATTTTCGG                         GCCGGATGACACTCCCTGGGATGGAG
genomic: GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG
EST: gi|169115251|gb|FE515641.1|FE515641
EST:     GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGG                         GCCGGATGACACTCCCTGGGATGGAG
genomic: GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG
EST: gi|169083954|gb|FE493594.1|FE493594
EST:     GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGG                         GCCGGATGACACTCCCTGGGATGGAG
genomic: GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG
EST: gi|169092766|gb|FE494943.1|FE494943
EST:     GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGG                         GCCGGATGACACTCCCTGGGATGGAG
genomic: GGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 34 (downstream exon)
Score: 81

TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG




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