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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcggcaaatcttctttactcatttcgttatgcacttttctgcat...

Basic information

species Physcomitrella patens
transcript PP1S212_85V6.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcgg---caaatcttctttactcatttcgttatgcacttttctgcat
 ||| |  | ||| |||| || || ||  | |||||||| || || |||||||| || || |||||||||||||| ||||| || ||||||||||||||||||     |  | ||| |       |  |   | | |  ||   || || |    ||  |   |    |   |  |   |||| |   |  | | |  | | |
GCACCAGGACGTCGACATCGTCGTCATCAGGGAGAACACCGAGGGGGAGTACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggcc--aatctcgcgtgacgcgcgctttgctctgtt-gttgtgtgttggttggagaatcgccacccgtgcatcgattttgacgtctaatgtgttcctt

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacaca-atttaatgc-gtatgaactgcggcaaatct-tctttactcatttcgttatgcacttttctgcat---
 ||||| || ||| ||||||| || ||  | |||||||| || || |||||||| || |||||||||||||||||||| || || || |||||||| ||||||  |  |  ||||      | | |   |||  |||  | || |||  || |   |   ||    |   |   | |   |  ||  |    |     ||||    
GCACGACAACGTCGACATTGTCGTCATCAGGGAGAACACCGAGGGCGAGTACTCCGGGCTTGAGCACGAGGTCGTCCCTGGCGTCGTGGAGAGCCTTAAGgta--tggcgaattccg----cttgctgctaactcacctagttgatgtagtgtttgccagggtgcttgggttaatgcgtgtgccgagagaaccccaaatgcaactt

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaatt---atcttattcttgaacc--ctacaagtaatacacaatttaatgcgtatgaactgcggcaaatcttctttactcatttcgttatg-cacttttctgcat
 |||||   |||| |||| || || ||  | |||||||| || || |||||||| || || |||||||||||||| |||||||| || ||||||||||||||| |    |   |    | |   |  || |   | ||    | | | ||   |  ||  ||    |   | || ||    ||     |||| |||  ||      
GCACGAGGGTGTCGACATCGTCGTAATCAGGGAGAACACCGAGGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTACCCGGGGTCGTTGAGAGCCTCAAGgtactacggagtgtcggttggggtcggctgcgtttcatgtttattatgatttttccgatatgttatactccctccttttatataagtatatgacaccgtt------

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA11G08920.1 (Glycine max), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaatta-tcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcggcaa-atcttctttactcatttcgttatgcacttttctgcat---
|||||| || ||  |||| || || ||  | |||||||| || || |||||||| || || || ||||||||||||||||| || ||||| |||||||||||| | | ||   |||  |    ||     |  | | |||  |||    ||  | |||    |  |  || | |  || |      ||| | ||    | ||   
CCACGACAACGTTGACATCGTCGTCATCAGGGAGAACACCGAGGGCGAGTACTCCGGCCTCGAACACGAGGTCGTCCCCGGCGTGGTCGAAAGCCTCAAGgtactcactcacgttcacggtttct-----ttctgctcaagctaaataatagcagctgaataattaggttttatgatcttaataaaatgaaattaagagaatgaa

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgta-attatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcggcaaatcttctttactcatttcgttatgcacttttctgcat--
||| ||||||||  | || || || ||  | |||||||| ||||| || |||||||| || || ||||||||||| ||||| ||||| || ||||| |||||   || |   | ||      | | |   | |  |    | ||     |   |  ||      || || ||   | ||||  ||||    ||||     |  
CCATGATAATGTGGATATCGTTGTCATCAGGGAGAACACCGAAGGCGAATACTCTGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtgcgttcttccactcccctcgctttc---tcacgctttttatatattatcaaatttgttttctatgtttttctattatttatttatttgtttttgaaattag

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaact-gcggcaaat-cttctttactcatttcgttatgcacttttctgcat---
||| ||||||||  | ||||| || ||  | |||||||| ||||| |||||||| || || || ||||||||||| ||||| ||||| || ||||| |||||  |  ||||  |||    | ||     |   ||||  ||||     || |  || ||      | ||  || ||  | |       | | |  | | | |   
CCATGATAATGTTGATATTGTTGTCATCAGGGAGAACACCGAAGGCGAGTACTCCGGCCTCGAACACGAGGTCGTTCCCGGCGTTGTTGAAAGCCTTAAGgtg-tgctcttcctctc---ctctcgctttctcacacttttta-catatagggtcttgctaagggtactagttaacgaactaaaaagagaaatcatttactttga

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcggcaaatcttctttactcatttcgttatgcacttttctgcat--
 ||||| |||||  | || || || ||  ||||||||||||||||||||||||| ||||| ||||| ||||| || || || |||||||||||||| |||||||  | | |||              | | |||   | | |  |  ||   || || |      ||| | ||  |||   ||| |  | || | ||  |  
ACACGAAAATGTTGATATCGTTGTGATAAGAGAGAACACTGAAGGAGAGTACTCAGGTCTCGAGCATGAGGTTGTTCCTGGTGTTGTCGAGAGCCTTAAGgtaa--accatatat------------aattatagggattgtttttagtccaaattgtgatc--ccttttgtatacatgatgttgttgaattgtttgtgtag

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaattta-atgcgt---atgaactgcg---gcaaatcttctttactcatt--------tcgttatgcacttttctgcat------
||| || |||||  |||| || || ||  |||||||||||||||| |||||| | || |||||||||||||| || || || || || ||||| || ||||| |  ||     | |     ||| |   |   |  |||| |  ||  ||   || | || ||   |||| |  |||||     ||        | ||| ||  | | | |  ||      
CCATGAGAATGTTGACATCGTTGTCATCAGAGAGAACACTGAAGGTGAGTACGCGGGGCTTGAGCACGAGGTTGTTCCTGGTGTCGTTGAGAGTCTGAAGgtgagaattccgatttctgctcct-cgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttag

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcggcaaatcttctttactcatttcgttatgcacttttctgcat-
 ||| || ||||  | ||||| ||  |  | |||||||| || || |||||| |||| ||||||||||||||||| ||||| || ||||| ||||| |||||||   |||  ||      |   | || |  |  |  ||  ||       ||  |  ||      ||   ||   |      |||  | |      | | 
GCACAATGATGTTGATATTGTTGTGGTGAGGGAGAACACGGAGGGCGAGTACGCTGGGCTTGAGCACGAGGTCGTTCCCGGCGTGGTCGAAAGCCTTAAGgtaac-gtctgtttggatgcctagagaactggtggaacataaaagaaaatagacttttggttctgttttggtaagaaaaaaaatataaaatgcgaccccta

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcgg--caaatcttctttactcatttcgttatgcacttttctgcat---
 ||| | |||||  | || || || ||||| ||||| || ||||| |||||||| || || |||||||||||||| ||||| || || || ||||| |||||  | || || || ||  ||| |     | ||    | |||      |    | ||| |  ||| | | |||| |||  ||    | | |          |   
GCACCAGAATGTGGATATAGTCGTGATTCGGGAGAATACGGAAGGCGAGTACTCGGGGCTCGAGCACGAGGTCGTTCCCGGTGTCGTGGAAAGCCTTAAGgttttgat-ttgttatt--accttgtc--tgatggttattttggccgtttcccaatgctgttcaattttccttttctcgattttagaggtagaggatcatttggt

upper sequence: PP1S212_85V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ13705 (Selaginella moellendorffii), 5'ss of exon 1
CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatcttattcttgaaccctacaagtaatacacaatttaatgcgtatgaactgcggcaaatcttctttactcatttcgttatgcacttttctgcat
||| || || ||||||||||| || || || |||||||| || || |||||| | || || ||||||||||||||||| || |||||||||   ||||||||| |   |   |||||   | || |      | | |         ||    | || ||     ||||    ||                          
CCATGACAACGTCAACATTGTTGTGATCCGGGAGAACACCGAGGGGGAGTACGCCGGCCTGGAGCACGAGGTCGTCCCGGGTGTTGTCGAGTCTCTCAAGgtactc--caatttcttctcctctgct----ttgctcggc------cgctccagctacgtttcttcttgcgcaccag-----------------------

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|67698118|gb|BJ958351.1|BJ958351
EST:     ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
EST: gi|208356872|gb|DC926883.1|DC926883
EST:     ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
EST: gi|67692443|gb|BJ952676.1|BJ952676
EST:     TCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: TCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
EST: gi|208373524|gb|DC941093.1|DC941093
EST:     ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
EST: gi|162265636|gb|FC441092.1|FC441092
EST:     ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAG                         GTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT
genomic: ACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTAT

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: 27 (upstream exon), 31 (downstream exon)
Score: 6

CCACGATAATGTCAACATTGTGGTTATTCGAGAGAACACTGAAGGAGAGTACTCTGGTCTTGAGCACGAGGTCGTCCCCGGGGTTGTCGAGAGCCTCAAGgtaattatct ... agcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA




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