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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCTCTACTGTGAAGGCGCTGGACGCCCTTGGCTTGGATGTACAACAGGCTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtctttcgcctcaagaattcgatgtgattgcaactaatagagtttgtgcgttgacatgggcgggaaatgtacatcggttgtcttatttagctgtgttaggcctcaagctgaagatcaccttgggtgtgggttattgctgtgggcag

Basic information

species Physcomitrella patens
transcript PP1S51_178V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S51_178V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 3
CCTCTCTACTGTGAAGGCGCTGGACGCCCTTGGCTTGGATGTACAACAGGCTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtctttcgcctcaagaattcgatgtgattgcaactaatagagtttgtgcgttgacatgggcgggaaatgtacatcggttgtcttatttagctgtgttaggcctcaagctgaagatcaccttgggtgtgggttattgctgtgggcag
 ||||| ||  ||| ||| ||||||  |||||| |||||  | || |||||||||||||||||||||||||| || ||  | ||  | ||| | || ||||||    |||| |   | |  |   |  |  |  | |   |  |    ||  ||| ||   |  |     ||||  | ||   |||| |  | |     || ||                                                
GCTCTCCACAATGAGGGCTCTGGACAACCTTGGATTGGACATCCAGCAGGCTGTCATCAGCTGCTTCAATGGGTTTGCATTGGATGTATTCAGAGCTGAGgtatacttcttcc--tttatcaccacctttagggtcctttttgt----ttaatgctttagtaaagattcaaaataaa-at--attgtttagtatgttcatggtacaatc-------------------------------------------

upper sequence: PP1S51_178V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ29742 (Selaginella moellendorffii), 5'ss of exon 3
CCTCTCTACTGTGAAGGCGCTGGACGCCCTTGGCTTGGATGTACAACAGGCTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtctttcgcctcaagaattcgatgtgattgcaactaatagagt-ttgtgcgttgacatgggcgggaaatgtacatcggttgtcttatttagctgtgttaggcctcaagctgaagatcaccttgggtgtgggttattgctgtgggcag
 ||||| ||  |||  || ||||| |  |||||| |||| || || |||||||| ||||||||||||||||| |||| ||| ||| |||| ||||| ||||||  |||  |      |     |    ||  | ||  | |  | |  | || |||                                                                                                 
GCTCTCCACAATGAGAGCTCTGGATGATCTTGGCCTGGACGTCCAGCAGGCTGTTATCAGCTGCTTCAATGGCTTCGTCCTCGACGTCTTTCGTGCCGAGgtataagttctcttttcc-----tctcgtgcaaatggtaatggtggcttgttttgcag-----------------------------------------------------------------------------------------------

upper sequence: PP1S51_178V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ28242 (Selaginella moellendorffii), 5'ss of exon 3
CCTCTCTACTGTGAAGGCGCTGGACGCCCTTGGCTTGGATGTACAACAGGCTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtctttcgcctcaagaattcgatgtgattgcaactaatagagtttgtgcgttgacatgggcgggaaatgtacatcggttgtcttatttagctgtgttaggcctcaagctgaagatcaccttgggtgtgggttattgctgtgggcag
 ||||| ||  |||  || ||||| |  |||||| |||| || || |||||||| ||||||||||||||||| |||| ||| ||| |||| ||||| ||||||  |||  ||    |      ||         ||||| |  ||  | | |   ||| |   |                                                                                        
GCTCTCCACGATGAGAGCTCTGGATGATCTTGGCCTGGACGTCCAGCAGGCTGTTATCAGCTGCTTCAATGGCTTCGTCCTCGACGTCTTTCGTGCCGAGgtataagttctttttttgttctcttttcctctcgtgcaaatggtaatggtggcttgtttagcag----------------------------------------------------------------------------------------

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|162186810|gb|FC363054.1|FC363054
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162192793|gb|FC369631.1|FC369631
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162192792|gb|FC369630.1|FC369630
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|208372882|gb|DC956283.1|DC956283
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162231249|gb|FC407023.1|FC407023
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162186811|gb|FC363055.1|FC363055
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162170259|gb|FC347379.1|FC347379
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162170260|gb|FC347380.1|FC347380
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162201436|gb|FC377162.1|FC377162
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162204865|gb|FC381196.1|FC381196
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|208388866|gb|DC945442.1|DC945442
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162175654|gb|FC351241.1|FC351241
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|67723820|gb|BJ974079.1|BJ974079
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162231250|gb|FC407024.1|FC407024
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162200058|gb|FC376520.1|FC376520
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
EST: gi|162200059|gb|FC376521.1|FC376521
EST:     CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAG                         GCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC
genomic: CTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTC

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), 35 (downstream exon)
Score: 4

CCTCTCTACTGTGAAGGCGCTGGACGCCCTTGGCTTGGATGTACAACAGGCTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtct ... ctgtgggcagGCCAAAGATGTGGACGTTGGACCAGAAGAAATAAAGGCCGTTCTGCTGCTCACTGCGGGATGTGATTTGCACTCTTTGCAGTAGATCCCACAATGCAGAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCTCTACTGTGAAGGCGCTGGACGCCCTTGGCTTGGATGTACAACAGGCTGTCATCAGCTGCTTCAATGGTTTCGCCCTTGACCTCTTCCGTGCAGAGgtaagagtctttcgcctcaagaattcgatgtgattgcaactaatagagtttgtgcgttgacatgggcgggaaatgtacatcggttgtcttatttagctgtgttaggcctcaagctgaagatcaccttgggtgtgggttattgctgtgggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT