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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattttgtgcgctaatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg...

Basic information

species Physcomitrella patens
transcript PP1S79_167V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os08g12840.1 (Oryza sativa), 5'ss of exon 3
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattttgtgcgctaatctcaatgtgaaggtgaaatta--gactgcaatttacttctagggcatattgcgatagcatga-cagttttattggttg
 || |  |  || |  || ||||| || || || ||||| || ||||||||||| || |||||| | ||||| || ||||||||||| |||||| |||||||  ||   || | | |  ||  |||    ||    | | |||||    | |  |  |  | |||   |  |  || | |   || | |  |  |  ||||  
AGAATATGCAGTTGGGATCAAGAATGTCACGATAAATGATAACTTCTTCCCTGGGCATTTCCCCGAACGACCCATAATGCCTGGTGTTCTCATGGTTGAGgtatgattccactatattggc--atccatgtgctgtgatcaaattgtttagtatatatggcctctgttgtttcctgaggtttgatcatctctcattgtggtc-

upper sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT2G22230.1 (Arabidopsis thaliana), 5'ss of exon 3
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagac--agcattt-----tgtgcgctaatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg
 |  |||| ||| || |||||||| || || ||||||||||||||||||||||| || |||||  | ||||| |||||||||||||| |||||| ||||||| | |   | | |||     ||    ||  | ||     |||| | |||| |   || |||| |  | |  |   | |||   |    | | | |  | |      
TGTTTCAGCTGTAGCTATTAAGAATGTCACCATCAATGACAATTTCTTCCCTGGCCATTTCCCTGAACGACCAATCATGCCTGGTGTTCTCATGATTGAGgtaataataatcgtttaaagttgcaaacttttgtcctcaagaagatcaaat-attttgtaattgatatgttagc--tgttgtattcctttcaaaatgctttaa----

upper sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT5G10160.1 (Arabidopsis thaliana), 5'ss of exon 3
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattt----tgtgcgctaatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg
 |  || |  || || ||||| ||||| || || |||||||||||||| ||||| || |||||  || ||||||| |||||||| || |||||| ||||||| |    ||||||    | | | ||  ||| | |   || ||  |||  |  ||||   ||  | ||  |   |  | ||     |   ||  |      || 
TGTATCTGCGGTAGCTATTAAAAACGTTACCATTAATGACAATTTCTTTCCTGGGCATTTCCCTGAGAGACCTATAATGCCTGGAGTTCTCATGGTTGAGgtaattt-gcatttgccctattctctcttcttactccaaaagttcaatctgtttgca---tatatttatagttaaaagagaagctttttgagcctagacattta

upper sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv00s0357g00020.t01 (Vitis vinifera), 5'ss of exon 3
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattttgtgcgctaatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg--
|   ||||  || || |||||||| |||||||| || || || ||||| ||||| ||||||||  || | || || |||||||||||||||||| ||||||| |        ||      ||  ||    | |  |  |||| | |   | | |   | |   ||   || ||   | |  |    | |     |  |||  
GATCTCAGCAGTAGCAATTAAGAATGTGACTATAAACGATAACTTCTTTCCTGGGCACTTCCCTGAGAGGCCAATTATGCCTGGTGTGCTCATGGTTGAGgtaatttgcttattgccaaact--tcatgttcttcatttgaattcaatttactagaaaataacagaaaatgtttgaaaaataaagaactcaacatatttgtg

upper sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EDP03190 (Chlamydomonas reinhardtii), 5'ss of exon 2
-----------------GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattttgtgcgc-taatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg
                 | |||  | ||| | |   |||   || || || || ||||| |||||||| || ||||||||| |||| |||||||||||||||| |    | ||||   | || ||||   | ||  |    ||  |  || | | |   || ||| ||| |          ||    ||  ||| |  ||    | ||  |||     
GTTGAGTGGGAGAAGGAGAAGTACGCTGTGGGCTACAAGTGTGTCACCATTAACGACAACTTCTTCCCAGGCCACTTCCCCGAGCGCCCTATCATGCCTGgtgagtgacttcttggcatcag-cagcgactcgtctgggccatggcggtgcgcacgc--aactag-ctgta---------cagatgctacagcgctgtcagcctacttgaatt-----

upper sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ31102 (Selaginella moellendorffii), 5'ss of exon 2
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattttgtgcgctaatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg
 |   | |  || |  ||||| |||||||| |||||||||||||||||||| || ||||| ||  || |||| ||||||||||| || |||||| ||||||| ||| | |  |  |   |  ||| |   || | || |  |||  |         | ||| ||   | | |  | |                       
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgt-agaaaacgatgagacagagaattttcttgcgtagttctaatacgttca-----tgcttttaaatcttctgtccag----------------------

upper sequence: PP1S79_167V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ06529 (Selaginella moellendorffii), 5'ss of exon 3
GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagcattttgtgcgctaatctcaatgtgaaggtgaaattagactgcaatttacttctagggcatattgcgatagcatgacagttttattggttg
 |   | |  || |  ||||| |||||||| |||||||||||||||||||| || ||||| ||  || |||| ||||||||||| || |||||| ||||||| ||| | |  |  |   |  ||| |   || | || |   ||     || |||||   || ||                                   
TGTCACGGCAGTAGGGATTAAAAACGTGACGATCAATGACAATTTCTTCCCCGGCCACTTTCCGGAGAGACCGATCATGCCTGGAGTTCTCATGGTTGAGgt-agaaaacgatgagacagagaattttcttgcgtagttctcatgcttttgaaatttctgtccag-----------------------------------

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|208375105|gb|DC956459.1|DC956459
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|162259266|gb|FC436183.1|FC436183
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|162259265|gb|FC436182.1|FC436182
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|18335736|gb|BJ167757.1|BJ167757
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|208387968|gb|DC932892.1|DC932892
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|67574481|gb|BJ947305.1|BJ947305
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|162276167|gb|FC452859.1|FC452859
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|67568985|gb|BJ941809.1|BJ941809
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|67692202|gb|BJ952435.1|BJ952435
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|162273717|gb|FC449440.1|FC449440
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|162176471|gb|FC353864.1|FC353864
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|67697899|gb|BJ958132.1|BJ958132
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|162273716|gb|FC449439.1|FC449439
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
EST: gi|162187843|gb|FC364417.1|FC364417
EST:     CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAG                         GCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT
genomic: CTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGT

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: 31 (upstream exon), 35 (downstream exon)
Score: 4

GGAGTCAGTTGTCGCCATTAAGAACGTGACTATCAATGACAATTTCTTCCCTGGTCACTTCCCCCAGCGACCTATCATGCCTGGTGTGCTCATGCTTGAGgtgagacagc ... gtgagtgtagGCTATGGCGCAGGCAGCAGGCATTATGATGCTGCAGCCGGAAGTTGGAGGTTCGAAGGAGTCGTTCTTTTTTGCCGGAGTGGATAAAGTGCGATTCCGGA




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