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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATTCCTGAACTAAGACATTATGCGCCATCTGTGCCTATCATCCTCGTGGGAACGAAACTAGgtccgtacctttacttgccacaataatcttatcgaagtgttctgtatcgaggttgattcgcatattcttagattgcaacataggcaatgtcttattatgt...

Basic information

species Physcomitrella patens
transcript PP1S257_74V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S257_74V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv10s0003g00570.t01 (Vitis vinifera), 5'ss of exon 4
TGGATTCCTGAACTAAGACATTATGCGCCATCTGTGCCTATCATCCTCGTGGGAACGAAACTAGgtccgtacctttacttgccacaataatcttat-cgaagtgttctgtatcgaggttgattcgcatattcttagattgc--aaca--taggcaatgtcttattatgt------------------------------------------------------
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TGGATTCCTGAACTGAGACATTATGCACCAACTGTGCCAATTGTGCTGGTGGGAACCAAACTTGgtaag-atgaatcttttcaacaagaattacagacagagaaactgatagccactgtggcaacattatttttaggccacttgacaattgaacaaaactttttcttcaaatttcaatacttgattgatattgacaagaaatctgaccatggcccaagtgcag
















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|100403655|gb|BY955035.1|BY955035
EST:     AAGACATTATGCGCCATCTGTGCCTATCATCCTCGTGGGA-CGAAACTAG                         ATCTTCGAGACGACAAGCAGTTCTT
genomic: AAGACATTATGCGCCATCTGTGCCTATCATCCTCGTGGGAACGAAACTAGgtccgtacct ... caattggcagATCTTCGAGACGACAAGCAGTTCTT
EST: gi|162169156|gb|FC345123.1|FC345123
EST:     AAGACATTATGCGCCATCTGTGCCTATCATCCTCGTGGGAACTAAACTAG                         ATCTTCGAGACGACAAGCAGTTCTTCGCTGATCATCCAGGAGCGGCTCCAA
genomic: AAGACATTATGCGCCATCTGTGCCTATCATCCTCGTGGGAACGAAACTAGgtccgtacct ... caattggcagATCTTCGAGACGACAAGCAGTTCTTCGCTGATCATCCAGGAGCGGCTCCAA

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: 12 (upstream exon), 26 (downstream exon)
Score: 3

TGGATTCCTGAACTAAGACATTATGCGCCATCTGTGCCTATCATCCTCGTGGGAACGAAACTAGgtccgtacct ... caattggcagATCTTCGAGACGACAAGCAGTTCTTCGCTGATCATCCAGGAGCGGCTCCAATAACTACCTCTCAA




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