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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGATGGCTGTTGGAGGTCTCCTCGCGTACAACTATTTGTTCCCTTCAGACGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCAgtaagttaccattctttctctttctcttttttttcgttatctgatgaaaacttttctgctgggtttgtag

Basic information

species Selaginella moellendorffii
transcript EFJ17355
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17355 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os05g33520.1 (Oryza sativa), 5'ss of exon 2
TCGATGGCTGTTGGA-GGTCTCCTCGCGTACAACTATTTGTTCCCTTCAGACGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCAgtaagttaccattctttctctttctcttttttttcgttatctgatgaaaacttttctgctgggtttgtag------------------------------
|| ||| |||||||  ||   |||  | | |||     ||||||| ||  | ||||| || |||  ||| |||||||||||||||||| | |||||||||||||||| |  |||   | | |    ||| |  ||    |     |  | || ||| |     |||   |                               
TCCATG-CTGTTGGGTGGAGCCCTTTCCTTCAATCTCGTGTTCCCGTCGAATGAGCCGGACATTTGGAGGCTGATGGGAATGTGGTCCATCTGGATGTTCAgtaagtaagaatttgatttgtggtacttgtcgttgtgcagtaagtttatacgtttgtaaattgttcccatcagcagcaaggattatgatctatccatgca

upper sequence: EFJ17355 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA19G33510.1 (Glycine max), 5'ss of exon 2
TCGATGGCTGTTGGAGGTCTCCTCG-CGTACAACTATTTGTTCCCTTCAGACGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCAgtaagttaccattctttctctttctcttttttttcgttatctgatgaaa----acttttctgctgggtttgtag--------------------------
|| |||  |||||| ||   | | | | |  ||     | |||||||| || || ||||| |||  |||| | ||||||||||||||| | |||||||||||||||||      ||  |  ||||  | |   ||| || |   ||||||    |  |   |||| | ||| |                            
TCAATG-TTGTTGGGGGGAGCTTTGTCTTTTAATCTCATCTTCCCTTCTGATGAACCTGACATTTGGAGATTAATGGGAATGTGGTCCATTTGGATGTTCAgtaagttctttacctgccaatttcgttctggattcattgttgtatgaaacaacaagtgcttgcttgctttctgcttcatgctttgccacttaccattttt

upper sequence: EFJ17355 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA03G30610.2 (Glycine max), 5'ss of exon 2
TCGATGGCTGTTGGAGGTCTCCTCGCGTACAACTATTTGTTCCCTTCAGACGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCAgtaagttaccattctttctctttctcttttttttcgttatctgatgaaaacttttctgctgggtttgtag------------------------------
|| |||    | |||||     |  | |  ||     | |||||||| || || ||||| |||  |||| | ||||||||||||||| | ||||||||||||||| |      ||| |  ||||  | |   ||| || |   ||||||         || | ||  |                                
TCAATGTTGTTGGGAGGAGCTTTGTCTTTTAATCTCATATTCCCTTCTGATGAACCTGACATTTGGAGATTAATGGGAATGTGGTCCATTTGGATGTTCAgtaagatttttaccttccaatttcgttctgaattcattgttgtatgaaacaacaagcacttgcttgctgctgcatgctttgccccttaccattctgtgta

upper sequence: EFJ17355 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S504_13V6.1 (Physcomitrella patens), 5'ss of exon 2
TCGATGGCTGTTGGAGGTCTCCTCGCGTACAACTATTTGTTCCCTTCAGACGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCAgtaagt--taccattctttctct----ttctcttttttttcgttatct--gatgaaaacttttctgctgggtttgtag----------------------
   |||   || || ||  || |  | | ||| |   | |||||||| ||| | || ||||||  | | || ||||| |||||||| |||||||||||||||||||  ||| |   |   | |    |      |||||| ||||| |    |   ||  |||       | ||  |                       
AGCATGCTCGTAGGCGGAATCTTGTCATTCAATTTGCTCTTCCCTTCTGACCATCCAGATATTTGGCGCCTCATGGGCATGTGGTCTGTGTGGATGTTCAgtaagtgctacaaacttggatatgaggtctagcatttttttgttatttttatttggaatgtttacatcatgattcaatctgttgtgaatgcaaaattcac

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|169054952|gb|FE461879.1|FE461879
EST:     CGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCA                         CAATTCCATCGCTTCGAGCAAGAGACTGCTCGTCTAAAGAGAAGGATGCTT
genomic: CGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCAgtaagttacc ... gggtttgtagCAATTCCATCGCTTCGCGCAAGAGACTGCTCGTCTAAAGAGAAGGATGCTT
EST: gi|169071552|gb|FE479126.1|FE479126
EST:     CGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCA                         CAATTCCATCGCTTCGAGCAAGAGACTGCTCGTCTAAAGAGAAGGATGCTT
genomic: CGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCAgtaagttacc ... gggtttgtagCAATTCCATCGCTTCGCGCAAGAGACTGCTCGTCTAAAGAGAAGGATGCTT

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: 29 (upstream exon), 9 (downstream exon)
Score: 3

TCGATGGCTGTTGGAGGTCTCCTCGCGTACAACTATTTGTTCCCTTCAGACGAGCCTGATATTGCGAGACTGATGGGAATGTGGTCCGTGTGGATGTTCAgtaagttacc ... gggtttgtagCAATTCCATCGCTTCGCGCAAGAGACTGCTCGTCTAAAGAGAAGGATGCTTTGAATTATTTGTTCTTGGCACTTCCGCTTGTCAACGTTTTGCTCCCATT




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