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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctcttctcttgtttggagtgtttggagtgttttctctaatttttttttctctttgttcttttttctggtgcgtgtag

Basic information

species Selaginella moellendorffii
transcript EFJ25138
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25138 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 1
AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctcttctcttgtttggagtgtttggagtgttttctctaatttttttttctctttgttct-----tttttctggtgcgtgtag------------------------------
 ||||||||   ||| |||||||||||| |||| || || |||||||||||||||||||||||     | ||  |||| || |  || ||| | || |||||         |||||   |      |   |      |||   | ||| |  | |||| | | |||     || ||   |||| ||                                 
GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtctctctctctctctctctctctccgcccgcccctctttacatgattctactctctcctcgatctggtgcttgtttgagtgcctgcgctgatggcctaatgccctccttgcctcgcag

upper sequence: EFJ25138 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G112609_T01 (Zea mays), 5'ss of exon 1
AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctcttctcttgtttggagtgtttggagtgttttctctaatttttttttctctttgttcttttttctggtgcgtgtag---------------------------------------------------------------------------------
 ||||||||   ||| |||||||||||| |||| || || |||||||||||||||||||||||     ||||  |||| || |  || ||| | || || |||    |||| |     | |       |     | | |       | | | | ||||| | |   | | ||   ||  |                                                                                     
GATGGCGCAGGCGGTGGAGGAGTGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCTGTCGTCACCACCGTCGGCTGCACCCTCGAAgtaccggctctccctccctctctctctctctctctctctctctctctctctctctctctctctctctctctcccatgactaggaaattcttctctttcgcccctgttgctaggatctctaatttgcgctctttacgtgcgcccgttggctgggccggctgtgcag

upper sequence: EFJ25138 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G082976_T01 (Zea mays), 5'ss of exon 1
AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctcttctcttgtttggagtgtttggagtgttttctctaatttttttt-------tctct----ttgttcttttttctg-gtgcgtgtag-------------------
 ||||||||   ||| ||||| |||||| |||| || || |||||||||||||||||||||||     | ||  |||| || |  || ||| | || ||||||    ||   | ||  ||   |   |  ||||  | ||||||      | |        |||||    |  | ||||||| || | ||  || |                   
GATGGCGCAGGCGGTGGAGGAATGGTACCGGCAGATGCCCATCATCACGCGCTCCTACCTCACCGCCGCCGTCGTCACCACCGTCGGCTGCACCCTCGAGgtaccggcttccccctccttcccatgatcaggagattcttctctcgcccatgtcgccaggatctctaatctcatccttttttttgtgcgcccgttggctggccccggctgtgcag

upper sequence: EFJ25138 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S226_55V6.1 (Physcomitrella patens), 5'ss of exon 2
AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctcttctc--ttgtttggagtgtttgg-agtgtt----ttctctaatttttttttctctttgttcttttttctggtg----cgtgtag-----
 ||||| ||| | |||||||| ||||||| |||||| || |||||||||||||| || ||||| |||||||||||||| || ||||| || ||  | ||||||   || |||     || | |  | |||| |  || |||    |  |  ||        |    |||||| | | || | |     |  ||||     
CATGGCTCAACTAGTAGAGGACTGGTACAAGCAAATGCCCATCATCACGCGCTCGTATCTCACTTTGTCTGTGCTCACCACCGCTGGATGTGCTTTGGAGgtactctcactttctgtttctattaattgttagatagagttaagatgtttaaacccaggagttgtcttgttcgtgtctcagatattccctcgtagcgtag

upper sequence: EFJ25138 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S68_188V6.2 (Physcomitrella patens), 5'ss of exon 1
AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctcttctc--ttgtttg-------gagtgtttggagtgtt------ttctctaatttttttttctctttgttcttttttctggtgcgtgtag-
 ||||||||| |||| ||||| ||||||| |||||| || |||||||||||| | || ||||| ||||||||||| || |||||||| || || || ||||||      |||  |  |  |||        | |||||| ||| |||      | | ||  || | ||   ||| ||      ||   | |   |||   
GATGGCGCAACTGGTGGAGGACTGGTACAAGCAAATGCCCATCATCACGCGCACTTATCTCACTTTGTCTGTGCTTACCACTGCTGGATGTGCTCTTGAGgtatttctcctttccattcctttacgtagttgtgtgtttcgagggttgaagtctacactgtttgtattgggtctctgccacagttatggttctttgttca

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|169044530|gb|FE451115.1|FE451115
EST:     GCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAG                         GTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCAC
genomic: GCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctc ... gtgcgtgtagGTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCAC
EST: gi|169064366|gb|FE472033.1|FE472033
EST:     GCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAG                         GTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCAC
genomic: GCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctc ... gtgcgtgtagGTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCAC
EST: gi|169051522|gb|FE459757.1|FE459757
EST:     GCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAG                         GTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCAC
genomic: GCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctc ... gtgcgtgtagGTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCAC
EST: gi|169039143|gb|FE448298.1|FE448298
EST:     GCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAG                         GTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCAC
genomic: GCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctc ... gtgcgtgtagGTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCAC

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: 25 (upstream exon), 29 (downstream exon)
Score: 8

AATGGCGCAATTGGTAGAGGAGTGGTACAGGCAAATACCTATCATCACGCGCTCCTACCTCACATTGTCTGTGCTCACTACTGCTGGTTGCGCGCTAGAGgtaaaatctc ... gtgcgtgtagGTGATCTCACCTCTCAATGTATACCTGAACCCAATGCGCGTTGTCAAGCACTACGAAGTGTGGCGCTTGGTCACAAACTTCTTCTACTTTGGTCGACTTG




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