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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTTGTAGAGAAGCGAGAACTTATTGGCATGGCCCGGGCTACATCTGACCACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgcttctgaagctggttttatgctttaaatccagtgtccattttttgtgaatatatttaaatgtacagatattaccaattaatgatttttaaag...

Basic information

species Physcomitrella patens
transcript PP1S332_23V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S332_23V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA09G40890.1 (Glycine max), 5'ss of exon 6
CGTTGTAGAGAAGCGAGAACTTATTGGCATGGCCCGGGCTACATCTGACCACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtag--tctgcttctgaagctggttttatgctttaaatccagtgtccattttttgtgaatatatttaaatgtacagatattaccaattaatgatttttaaag-
 |     ||  ||     | | |||||||||||||| ||||| |||||||| ||||||||||| || |||||||| || || || |||||    || ||||||   |||| | |  ||  ||| ||  || |     |  | ||   |  ||        | | |  ||| | ||  | |    | |      ||  |  |  
GGGGAATGAACAGAAGAGATTAATTGGCATGGCCCGTGCTACGTCTGACCATGCCTTCAATGCCACAATTTGGGATGTCCTAGTTGATCCTGGCTACCAGgtattttctgttaccaaacatggattc-tgttgccggtt-actgaaaaagttaaccaccaaaagtggaatatgcat-tgtcctaagtctcaagttcatgtatt

upper sequence: PP1S332_23V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA18G44940.1 (Glycine max), 5'ss of exon 5
-CGTTGTAGAGAAGCGAGAACTTATTGGCATGGCCCGGGCTACATCTGACCACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagt--ctgcttctgaagctggttttatgctttaaatccagtgtccattttttgtgaatatatttaaatgtacagatattaccaattaatgatttttaaag
  |     ||  ||     | | |||||||||||||| ||||| |||||||| ||||||||||| || |||||||| || || || ||||||   || |||||| |  |||   |  ||  ||| |||   |  ||| ||  ||| |  ||  |    ||  ||   | |     | ||   |  |||   |  ||  |  | 
AGGGGAATGAACAGAAGAGATTAATTGGCATGGCCCGTGCTACGTCTGACCATGCCTTCAATGCCACAATTTGGGATGTCCTAGTTGATCCAGGCTACCAggtattttctgtcaccaaacatggatttgaacaataactctggtgccggttactgaaaaaattagcgacaaaagtatatgcaa--aatctctagttcatgta-

upper sequence: PP1S332_23V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv08s0056g00580.t01 (Vitis vinifera), 5'ss of exon 4
CGTTGTA-GAGAAGCGAGAACTTATTGGCATGGCCCGGGCTACATCTGACCACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgcttctgaagctggttttatgctttaaatccagtgtccattttttgtgaatatatttaaatgtacagatattaccaattaatgatttttaaag---
 |  | | ||| |     | ||||||||||||||||| |||||||| || || ||||||||||| || |||||||| || ||||| ||||| | |||||||||| ||| | | |     | |  ||       | |||| |  |       ||        ||||   |   ||||    |     |||| |  |  | |    
-GAGGAATGAGCAAAAGAAGCTTATTGGCATGGCCCGTGCTACATCAGATCATGCCTTCAATGCCACAATTTGGGATGTCCTTGTTGATCCTTCATATCAGgtattcttcatatc---tttgccttggaaaagagatcctggttgtggacatttaaggagaattttccttctcagacccaaaattgtaataacatgaacatgtt

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|37830115|gb|BJ588127.1|BJ588127
EST:     ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAG                         GGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
genomic: ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
EST: gi|162214828|gb|FC390963.1|FC390963
EST:     ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAG                         GGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
genomic: ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
EST: gi|162258040|gb|FC434134.1|FC434134
EST:     ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAG                         GGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
genomic: ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
EST: gi|162219571|gb|FC395567.1|FC395567
EST:     ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAG                         GGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
genomic: ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
EST: gi|162214827|gb|FC390962.1|FC390962
EST:     ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAG                         GGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
genomic: ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
EST: gi|37853342|gb|BJ611350.1|BJ611350
EST:     ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAG                         GGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
genomic: ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
EST: gi|18339971|gb|BJ171999.1|BJ171999
EST:     ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAG                         GGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
genomic: ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
EST: gi|208381568|gb|DC923154.1|DC923154
EST:     ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAG                         GGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA
genomic: ACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTA

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: 24

CGTTGTAGAGAAGCGAGAACTTATTGGCATGGCCCGGGCTACATCTGACCACGCCTTCAATGCTACCATTTGGGACGTGCTTGTAGATCCATTATATCAGgtagtctgct ... atatttgcagGGGCAAGGCTTAGGTAAGGCTTTAGTGGAGCAGATGATCCGGGCTTTGTTAAGAAGGGATATCGGCAACATCACACTCTTCGCCGACGCACAAG




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