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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGGTTACATTGCTGGAATTTTTTGCGCTCTCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatccttgtttcggtggtgtttctcgcgcttattaggctaaatgctcgttttattttgctccag

Basic information

species Selaginella moellendorffii
transcript EFJ31007
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31007 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os09g28160.1 (Oryza sativa), 5'ss of exon 3
TGGCGGTTACATTGCTGGAATTTTTTGCGCTCTCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatccttgtttcgg--tggtgtttctcgcgcttat--taggctaaatgc-tcgttttattttgctccag-------------------------------------
  | || |||||||||||| | || |||||   |||||||||||||||||||||| | |||||||| ||||||||  |||||| ||||||||||||  | ||| || | |    |   |   ||     |  |    |||  | | ||  |||| |  |   | | ||     |                                     
GAGTGGCTACATTGCTGGAGTCTTCTGCGCCGCCGTCTCGCACCCTGCTGACAACTTGGTCTCGTTTCTCAACAACTCCAAGGGCGCCACCGTTGGAGATgtaagtctgcaccctgtagaacggcacagccgggagctatacttgacttgatgcgttttgccaatgtgtgattgttttgtgttcgtttgctgaattcttatttcttttcag

upper sequence: EFJ31007 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os04g37600.1 (Oryza sativa), 5'ss of exon 4
TGGCGGTTACATTGCTGGAATTTTTTGCGCTCTCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatccttgtttcggtggtgtttctcgcg-cttattaggctaaatgctcgttttattttgctccag---
 || ||||||||||| ||  | || || ||  | || || |||||||| ||||| ||||| || |||||||||||| |||||| ||| || |||||| | ||| || |  |  |  |  |    | |   |   | | || |    | |  |  |||  | ||||        
AGGTGGTTACATTGCAGGGGTGTTCTGTGCAATAGTTTCACACCCTGCGGACAATCTTGTGTCTTTCCTCAACAATGCCAAGGGCGCAACAGTTGGCGATgtaagttttgtaatcaccataccatcttctgtaacgtgtttgttggatttattatttcttgttgcatttacag
















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|169070433|gb|FE476798.1|FE476798
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAA                         GCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
EST: gi|169035239|gb|FE442604.1|FE442604
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAA                         GCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
EST: gi|169104740|gb|FE508988.1|FE508988
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAA                         GCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
EST: gi|169092867|gb|FE496331.1|FE496331
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAA                         GCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
EST: gi|169061542|gb|FE469329.1|FE469329
EST:     ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAA                         GCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG
genomic: ACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTG

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: 21 (upstream exon), 26 (downstream exon)
Score: 7

TGGCGGTTACATTGCTGGAATTTTTTGCGCTCTCGTCTCGCACCCTGCTGACAACCTTGTCTCGTTCCTCAACAATACCAAGGACGCCACCGTTGGCCAAgtatgtatcc ... tttgctccagGCCGTCAAGAGCATGGGCCTGGTGGCTCTCGTCACCCGGGGGCTACCGCTGCGTATCGTGATGATTGGAACTCTCACTGGAGCGCAGTGGGTAATCTACG




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