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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCCAGCTGTTACAGATGTTGCTATTGCTGCACTTAATGGGTTGAAAATGGGTGACAAGACTTTAAGCGTGCGTCGTGCTTCTGCCAGgtagcgaattttttttaatctttctcaccctatccgtctgtatggctgtgtgcctcgttcccttccctttcacaggacccatcagttgtggatattgcct...

Basic information

species Physcomitrella patens
transcript PP1S58_254V6.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_254V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: Vv00s0561g00030.t01 (Vitis vinifera), 5'ss of exon 12
GATCCAGCTGTTACAGATGTTGCTATTGCTGCACTTAATGGGTTGAAAATGGGTGACAAGACTTTAAGCGTGCGTCGTGCTTCTGCCAGgtagcgaattttttttaatctttctcaccctatccgtctgtatggctgtgt-gcctcgttcccttccctttcacaggacccatcagttgtggatattgcct----
||||||||||| || ||  |||||  |||||| |||||||| |||||||||||||| |||||| | |  |||||||||||  | |   |||||    | | ||| | |   ||  ||  |    |      || |  ||| |  | |||   ||   ||  | | | ||   |    |      || |      
GATCCAGCTGTGACTGACATTGCTTGTGCTGCGCTTAATGGCTTGAAAATGGGTGATAAGACTCTTACAGTGCGTCGTGCCACAGTTGGgtag---gtgtctttgagtaaatcatacaatgattggaatcctgaccttgttgttttgttttgttt--ttcaataagtcctcgctacagcatgctttccaaactc

upper sequence: PP1S58_254V6.1 (Physcomitrella patens), 5'ss of exon 14
lower sequence: Vv00s0611g00010.t01 (Vitis vinifera), 5'ss of exon 3
GATCCAGCTGTTACAGATGTTGCTATTGCTGCACTTAATGGGTTGAAAATGGGTGACAAGACTTTAAGCGTGCGTCGTGCTTCTGCCAGgtagcgaattttttttaatctttctcaccctatccgtctgtatggctgtgt-gcctcgttcccttccctttcacaggacccatcagttgtggatattgcct----
||||||||||| || ||  |||||  |||||| |||||||| |||||||||||||| |||||| | |  |||||||||||  | |   |||||    | | ||| | |   ||  ||  |    |      || |  ||| |  | |||   |||  ||  | | | ||   |    |      || |      
GATCCAGCTGTGACTGACATTGCTTGTGCTGCGCTTAATGGCTTGAAAATGGGTGATAAGACTCTTACAGTGCGTCGTGCCACAGTTGGgtag---gtgtctttgagtaaatcatacaatgattggaatcctgaccttgttgttttgttttgttc--ttcaataagtcctcgctacagcatgctttccaaactc
















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|162183241|gb|FC360391.1|FC360391
EST:     GGGTTGAAAATGGGTGACAAGACTTTAAGCGTGCGTCGTGCTTCTGCCAG                         TGGACAGCCAAAGCCGGATCAAGCAAACGTTCTGGCTCACGCTCAGCAGCA
genomic: GGGTTGAAAATGGGTGACAAGACTTTAAGCGTGCGTCGTGCTTCTGCCAGgtagcgaatt ... tatgtttcagTGGACAGCCAAAGCCGGATCAAGCAAACGTTCTGGCTCACGCTCAGCAGCA
EST: gi|162184034|gb|FC359404.1|FC359404
EST:     GGGTTGAAAATGGGTGACAAGACTTTAAGCGTGCGTCGTGCTTCTGCCAG                         TGGACAGCCAAAGCCGGATCAAGCAAACGTTCTGGCTCACGCTCAGCAGCA
genomic: GGGTTGAAAATGGGTGACAAGACTTTAAGCGTGCGTCGTGCTTCTGCCAGgtagcgaatt ... tatgtttcagTGGACAGCCAAAGCCGGATCAAGCAAACGTTCTGGCTCACGCTCAGCAGCA
EST: gi|162244000|gb|FC422329.1|FC422329
EST:     GTCGTGCTTCTGCCAG                         TGGACAGCCAAAGCCGGATCAAGCAAACGTTCTGGCTCACGCTCAGCAGCA
genomic: GTCGTGCTTCTGCCAGgtagcgaatt ... tatgtttcagTGGACAGCCAAAGCCGGATCAAGCAAACGTTCTGGCTCACGCTCAGCAGCA

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), 23 (downstream exon)
Score: 5

GATCCAGCTGTTACAGATGTTGCTATTGCTGCACTTAATGGGTTGAAAATGGGTGACAAGACTTTAAGCGTGCGTCGTGCTTCTGCCAGgtagcgaatt ... tatgtttcagTGGACAGCCAAAGCCGGATCAAGCAAACGTTCTGGCTCACGCTCAGCAGCAAATCGCTATTCAG




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