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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGAATTCGTAATGACCAAGGATGAATTTTCTGGTGCTGACATTAAAGCCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgtcgtcttttgtactttgcagttcgtgaatggaggctaattgaccagctgaaatgaataaaagttgcttttgatcaaaagacctggtttcttgtaatgagttgttattgttttggatggtgatcttgcag

Basic information

species Physcomitrella patens
transcript PP1S12_207V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 5
GGAGGAATTCGTAATGACCAAGGATGAATTTTCTGGTGCTGACATTAAAGCCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgtcgtcttttgtactttgcagttcgtga-----atggaggctaattgaccagctgaaatgaataaaagttgcttttgatcaaaagacctggtttc--ttgtaatgagttgttattgttttggatggtga--tcttgcag----------------------------------------
 || || || || |||||||||||||| ||||||||||||||||| ||||| || || |||||||| ||  | || || ||  | |||||| | ||||||||||    |   | |||| |       | | | ||      |     | ||||     | ||     | |||  |  |||   |  |   |   |   ||||    ||   | ||    ||||    ||||  |  |    |||  |                                        
AGAAGAGTTTGTGATGACCAAGGATGAGTTTTCTGGTGCTGACATCAAAGCAATATGTACGGAGGCCGGATTGCTCGCTTTAAGGGAGCGCAGAATGAAGgtaactcagctttgttttctcaaccagactccttgctctctagtactgttaatgttaaaactttcgagcatactaagtgccaatcctttcagatctgagtttgagctgcgctcagaacatatttgcatggaatgcaagtctttgttgcacttctctttttacatttgctgttcttctgttgctttag

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 5'ss of exon 4
GGAGGAATTCGTAATGACCAAGGATGAATTTTCTGGTGCTGACATTAAAGCCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgtcgtcttttgtactttgcagttcgtgaatggaggctaattgaccagctgaaatgaataaaagttgctt-ttgatcaaaagacctggtttcttgtaatgagttgttattgttttggatggtgatcttgcag
||| || || || |||||||||||||| ||||| |||||||| || ||||| || || || || ||||| |||||||| ||| | || ||||| ||||||||| || ||     |||||| || |  | |     |||  |  ||  |     |||  || | |       |||  |  ||| | | | |||        |                                      
GGAAGAGTTTGTCATGACCAAGGATGAGTTTTCCGGTGCTGATATCAAAGCAATATGTACTGAAGCTGGACTTCTTGCTTTGAGAGAACGCCGAATGAAGgtatgagtgaacctttttgt-ctcta-attgaaataatcaaaccttttatgagagcccaatttagaccgttttgtctactgacctatataccaaacaatgtc-------------------------------------

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G104373_T01 (Zea mays), 5'ss of exon 5
GGAGGAATTCGTAATGACCAAGGATGAATTTTCTGGTGCTGACATTAAAGCCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgtcgtcttttgtactttgcagttcgtgaatggaggctaattgaccagctgaaatgaataaaagttgcttttgatcaaaagacctggtttcttgtaatgagttgttattgttttggatggtgatcttgcag
 || || ||  | ||| | || ||||| ||||| ||||||||||| || |||||||| || || |||||  | ||||| ||| | ||||| |||||||||||||||  |     |     |  |  |   |  ||  |     |  ||  | | |||    || || ||  ||| |  | | |  ||  | |   || || |                                    
AGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTACTGAAGCTGGCTTGCTTGCTTTGAGAGAGCGGCGGATGAAGgtaagacagctcagtacaccaaatacccccttctgtttttt--cccatgaatctgctactttggattaaccttgttggt-acctgaaaccgtcactttttttg-----------------------------------

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|37827368|gb|BJ585380.1|BJ585380
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|162233611|gb|FC409370.1|FC409370
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|67722661|gb|BJ972920.1|BJ972920
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|67721772|gb|BJ972031.1|BJ972031
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|208350798|gb|DC925929.1|DC925929
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|162179026|gb|FC356427.1|FC356427
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|208374231|gb|DC945277.1|DC945277
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|208372234|gb|DC948037.1|DC948037
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|208370715|gb|DC948252.1|DC948252
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|67723618|gb|BJ973877.1|BJ973877
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
EST: gi|208379248|gb|DC927259.1|DC927259
EST:     CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAG                         GTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG
genomic: CCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAG

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: 34 (upstream exon), 35 (downstream exon)
Score: 6

GGAGGAATTCGTAATGACCAAGGATGAATTTTCTGGTGCTGACATTAAAGCCATTTGCACGGAGGCTGGTCTTCTTGCGTTGCGTGAGCGCCGGATGAAGgtaagattgt ... gatcttgcagGTGACTCAAGTTGATTTCAAGAAGGCCAAAGAGAAGGTAATGTATAAGAAGAAGGAAGGTGTACCTGAGGGATTATACATGTAGATTATTCAGTGCAGGT




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