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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGATCGATCGAGGCAGGAGCTATGAGCCGAGGGAGTGGCGCTGGATACGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatctcagctcagcttacttagagtgccttagagcgctggatggatctcagtgattttgcgctcgttcttacttggcag

Basic information

species Selaginella moellendorffii
transcript EFJ09222
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ09222 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g08280.1 (Oryza sativa), 5'ss of exon 1
GATCGATCGATCGAGGCAGGAGCTATGAGCCGAGGGAGTGGCGCTGGATACGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatctcagctcagcttacttagagt---gccttaga-gcgctggatggatctcagt-gattttgcgctcgttcttacttggcag--------------------------------------------------
|      |||   |  | |   | |||||||| || |  ||||| || ||||| ||||||||||| |||||||| |||||||| |||||||| |||||||||| ||  ||||  | |   ||||| | |     ||||     || || | |    | |  | ||  ||      | | ||  |  |  |                                                  
GCGGCGGCGAGAAATCCGGCGACGATGAGCCGCGGCACGGGCGCCGGCTACGACCGCCACATCACCATCTTCTCCCCGGAGGGCCGCCTCTACCAAGTCGgtgcgtggtctcccccc---ttactaaaaccctagcctcgcccgccctcgtttttccccgctcgaggttagatctgctttttttgtgatgttgggaggctgatctgatctggtttgatctggtgttttggtgttgtgcag

upper sequence: EFJ09222 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G016511_T01 (Zea mays), 5'ss of exon 1
GATCGATCGATCGA-GGCAGGAGCTATGAGCCGAGGGAGTGGCGCTGGATACGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatctc----agctcagcttacttagagtgccttagagcgctggatggatct---cagtgattttgcgctcgttcttacttg-gcag--------------
    ||||   ||  ||| || |  |||||||| || |  ||||| || || || ||||||||||| |||||||| |||||||| ||||| || ||||||||||||||  | |    | |  |||    |       |||     ||||   | |||||     | |  ||||  |||  ||| || || || |              
-GGTGATCTTCCGGCGGCCGGCGAGATGAGCCGTGGCACAGGCGCGGGCTATGACCGCCACATCACCATCTTCTCCCCGGAGGGACGCCTGTACCAAGTCGgtgagtaccccccaaaaccctagccctttctttcctcctcgc--cgctccttagatctggaggggggatttgtactccatctgacctgtgccgttccgtgtgcgcag

upper sequence: EFJ09222 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S335_59V6.1 (Physcomitrella patens), 5'ss of exon 1
-GATCGATCGATCGAGGCAGGAGCTATGAGCCGAGGGAGTGGCGCTGGATACGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagt--aatctcagctcagcttactta------gagtgccttagagcg---ctggatg-gatctcagtgattttgcgctcgttcttacttggcag---
 | |    |   |||  |||||    |||| || ||    || ||||| || ||||| |||||||| || ||||||||||| ||||| || || |||||||||||||  |||    |  | | || | ||      | ||   || ||| |    || ||| ||     || |  ||    | |   |||||||| ||   
TGCTGCGCCAGCCGAATCAGGA----TGAGTCGTGGATCGGGGGCTGGGTATGATCGACACATCACTATTTTCTCGCCGGAAGGGCGTCTTTACCAAGTCGgtgagtggaattctcgtgctgtttgcgtatcgggtgggtatgttggagtgattttgtatgtgagagtcgtcagcttagtgttgggtttacttggaagacg

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|169048168|gb|FE455440.1|FE455440
EST:     CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCG                         AGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
genomic: CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatc ... tacttggcagAGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
EST: gi|169064643|gb|FE471374.1|FE471374
EST:     CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCG                         AGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
genomic: CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatc ... tacttggcagAGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
EST: gi|70670234|gb|DN838811.1|DN838811
EST:     CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCG                         AGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
genomic: CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatc ... tacttggcagAGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
EST: gi|169048167|gb|FE455439.1|FE455439
EST:     TCTATCAAGTCG                         AGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
genomic: TCTATCAAGTCGgtgagtaatc ... tacttggcagAGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
EST: gi|169050807|gb|FE459953.1|FE459953
EST:     CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCG                         AGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
genomic: CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatc ... tacttggcagAGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
EST: gi|169113460|gb|FE514995.1|FE514995
EST:     CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCG                         AGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
genomic: CGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatc ... tacttggcagAGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
EST: gi|169064642|gb|FE471373.1|FE471373
EST:     CGCCGGAGGGGCGCCTCTATCAAGTCG                         AGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC
genomic: CGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatc ... tacttggcagAGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCC

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), 35 (downstream exon)
Score: 78

GATCGATCGATCGAGGCAGGAGCTATGAGCCGAGGGAGTGGCGCTGGATACGATCGCCACATCACGATCTTCTCGCCGGAGGGGCGCCTCTATCAAGTCGgtgagtaatc ... tacttggcagAGTATGCATTCAAGGCTGCCAAGAGCCCGGGCATCACATCGATTGGTGTCCGTGGAGCAGACTCGGTGTGCGTGGTTACACAGAAGAAAGTCCCG




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