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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtcagtcttttttccgaggcttgatctgcttggttttgtacagaaacatgatgctgattgcgaccgtgtatcgcccaaagtgacgtttagacc...

Basic information

species Physcomitrella patens
transcript PP1S165_119V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 3
CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtcagtcttttttccgaggcttgatctgcttggttt-tgtacagaaacatgatgctgattgcgaccgtgtatcgcccaaagtgacgtttagacc
 ||| | || ||||| ||||| |||||||| || ||||||||||| ||||||||  | ||||| | ||||||||| ||||||||  ||||||| ||||||||      | || |||  ||   |  | | || |  ||  | | |  |   ||||||  || |   ||   | ||  |  |    |  |    |  | |  
TAGCTTGATCTTTGAATATGTCAACAATACAGACTTCAAAGTGCTGTACCCCACGTTGACAGATTATGATATCCGCTACTACATATATGAGCTACTCAAGgtcttcattgagccttcattgtcatccct-atttatttactctattcagtaaaacatcctgttctgtggatctgtagaatgatgtatctcttatagaaatt

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os03g55490.1 (Oryza sativa), 5'ss of exon 3
CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtcagtcttttt---tccgaggcttgatctgcttggttttgtacagaaacatgatgctgattgcg-accgtgtatcgcccaaagtgacgtttagacc
 ||  | || ||||| ||||| |||||||||||||||||||| |||||||| || ||    || |  |||||| ||||||||||| | ||  |  | ||||| | |  || |  ||      ||| | |  ||   |  |   | || |  |   |    ||  ||  |  | | | | | |         ||   ||| ||  
TAGTTTGATCTTTGAATATGTCAACAATACTGATTTCAAAGTACTCTACCCAACACTATTGGATTACGATATCAGATACTACATTTACGAATTATTAAAGgtaa-taatctgaattgcagaatcctatgtctgtaataatcaatgtttt-tatttatgctatcttgtctatggaacatttctttgtactgatggtattttga--

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 5'ss of exon 3
CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtcagtct--tttttccgaggcttgatctgcttggttttgtacagaaacatgatgctgattgcgaccgtgtatcgcccaaagtgacgtttagacc
 ||| | || |||||||||||||||| ||| |||||||||||  | ||||||||||| || || | ||| || || ||||||||  ||||||| |||||||| | |  |   |    ||| |  ||| | | |  |  |||  ||| |      |  | |  ||    |  |   ||   |   |    ||   |       
TAGCTTGATATTTGAGTATGTGAACAGTACAGATTTCAAAGTTTTGTACCCCACTCTGACCGATTATGACATACGCTACTACATATATGAGCTTCTCAAGgtaatttatactttagatttattagagacataacttttttgcctttctctcttcatctca-acttgcagaaattatgc-ccattcttgatgttttgctagtt

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv07s0129g00270.t01 (Vitis vinifera), 5'ss of exon 3
CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtcagtcttttttccgaggcttgatctgctt--ggttttgtacagaaacatgatgctgat-tgcgaccgtgtatcgcccaaagtgacgtttagacc
 || ||||| ||||| || ||||| ||||||||||| |||||||| || || |||||  |||||| |||||| ||||| |||||  |||| || || ||||| ||   ||  ||| | |  |         | | |||  | |  |||   ||| ||    |||  | ||| |  || |          |     | |     
AAGTCTAATATTTGAATACGTGAATAATACTGATTTTAAAGTGCTTTATCCAACTCTCTCAGACTATGATATTCGATATTACATCTATGAACTTCTAAAGgtaagatctctctctctctctctctctcatttttccttgcgataatgtgatgaagcacatggctagtgtgcaaaagtattctcttttctgcattatctct---

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|208360006|gb|DC939310.1|DC939310
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAAGGGATTATGCACANGGATGTGAAGCCA
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCA
EST: gi|100447198|gb|CJ971497.1|CJ971497
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAAGG-ANTATGCACAGGGATGTGAN-CCA
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCA
EST: gi|67709495|gb|BJ965311.1|BJ965311
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATT
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATT
EST: gi|100397857|gb|BY990436.1|BY990436
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTNCA-GGGATTATGCACAGGGATGTGAAAGC
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCT-CAAGGGATTATGCACAGGGATGTGAA-GC
EST: gi|100401634|gb|BY954629.1|BY954629
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGCGAAGCCA
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGATTATGCACAGGGATGTGAAGCCA
EST: gi|100436225|gb|BY979442.1|BY979442
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTCTCAGGGGAT
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTCTCAAGGGAT
EST: gi|67574586|gb|BJ947410.1|BJ947410
EST:     CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAG                         GCTTTGGACTATTGCCATTC
genomic: CCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtc ... attgttgcagGCTTTGGACTATTGCCATTC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCCTAATTTTTGAGTATGTGAACAATACTGATTTCAAAGTGCTCTACCCCACTCTTACAGACTTTGATATCCGATACTACATTCATGAGCTGCTCAAGgtgagtggtcagtcttttttccgaggcttgatctgcttggttttgtacagaaacatgatgctgattgcgaccgtgtatcgcccaaagtgacgtttagacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT