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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgttcacttttattatctctgttgtctttctaatgagttttgcttctggactgattttactacattatgagatttcactctcttgccttgtacgttattaatgtttttccaacagcttttgatgttcttttggattctcatcattgtcaacttacaatacgattgatcctgtttgatgcag

Basic information

species Physcomitrella patens
transcript PP1S366_17V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G177276_T01 (Zea mays), 5'ss of exon 6
TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgttcacttttattatctctgttgtctttctaatgagttttgcttctggactgattttactacattatgagatttc--actctcttgccttgtacgttattaatgtttttccaacagcttttgatgttcttttggattctcatcattgtcaacttacaatacgattgatcctgtttgatgcag
||||||| ||  ||||||||||||||||||||||| ||||||||     || |  |  |  || |   |||       ||||   | || || ||||       || |  |   | || |||    ||    | |  ||||| |  | ||                                                                                
TTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAGgtatgcacatttaact--agcatattacttg-------aatgtaatgtgtttttgga--agccatagtgtacctttagtttttcagctactgtacaatgtacatactcaaa-------------------------------------------------------------------------------

upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA07G05170.1 (Glycine max), 5'ss of exon 7
TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgttcacttttattatctctgttgtctttctaatgagttttgcttctggactgattttactacattatgagatttcactctcttgccttgtacgttattaatgtttttccaacagcttttgatgttcttttggattctcatcattgtcaacttacaatacgattgatcctgtttgatgcag
|||||||||| | ||||||||| ||||||||||| |||||||          | ||||| |      ||| | ||  | ||    ||| ||          |||||||   ||||      |    || ||||    |  |  ||| || | | |  || | |  |  ||||   ||   |||    | || |     |   |||    |  ||  | ||  ||||||
TTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAGgt-----cagaaagttttagttatgaagttcttttatttatacactttactatgttttgttttttactgttttatttaccctttgacttttgc---atgaggaattgatatctgtg-aataacagtaaatgtggattattattgct-ttatagctttatactaatgttttcaatttt-ttgaatgcag

upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA16G01680.1 (Glycine max), 5'ss of exon 7
TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgt------atttttgtt---cacttttattatctctgttgtctttctaatgagttttgcttctggactgattttactacattatgagatttcactctcttgccttgtacgttattaatgtttttccaacagcttttgatgttcttttggattctcatcattgtcaacttacaatacgattgatcctgttt---gatgcag
|||||||||| | ||||||||| ||||||||||| |||||||       |||| |||    | || | |||| | | || | |   |||||  ||    |  | |  |  |||||||   ||||      |    || ||||    |  |  ||| || | | |  || | |  |  ||||      ||||| | || | | |  |  |  |    |||   | |  |||    ||||||
TTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAGgtcagaaagttttagttgtgaagttcttttatttatattatatggttaatggtttaccatgtttggtt--ttttacttttttatttatcctttgacttttgc---atgaggaattgatatctgtg-aataacaataaatgt------ggattattattactttatagctttatactgatgttttcaatttccgaatgcag

upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ32150 (Selaginella moellendorffii), 5'ss of exon 6
TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgttcacttttattatctct-gttgtctttctaatgagttttgcttctggactgattttactacattatgagatttcactctcttgccttgtacgttattaatgtttttccaacagcttttgatgttcttttggattctcatcattgtcaacttacaatacgattgatcctgtttgatgcag
||||||||||||||||||||||||||||||| ||||||||||| | |  |  | | | |  |   || ||  | | | |   |  |||||   | |                                                                                                                                     
TTCATCCAGAGACTTGGAATCCAATGTGGTCAGTTTCAAGgtactgtcctagattgtcacgaaaacttgtcatttatttgtggccttttgtcgcag-------------------------------------------------------------------------------------------------------------------------------------

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|208387466|gb|DC949251.1|DC949251
EST:     TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG                         TATTTTGACTGGCCTTCTGTCTTTTATG
genomic: TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgt ... tttgatgcagTATTTTGACTGGCCTTCTGTCTTTTATG
EST: gi|208347731|gb|DC925604.1|DC925604
EST:     TTCATCCAGAGACTTGGAATCCCATGTGGTCTGTTTCNAG                         TATTTNGACTGGCCTTCTGTCTTTTATG
genomic: TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgt ... tttgatgcagTATTTTGACTGGCCTTCTGTCTTTTATG
EST: gi|162277893|gb|FC454356.1|FC454356
EST:     TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG                         TATTTTGACTGGCCTTCTGTCTTTTATG
genomic: TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgt ... tttgatgcagTATTTTGACTGGCCTTCTGTCTTTTATG
EST: gi|37829048|gb|BJ587060.1|BJ587060
EST:     TTCATCCAGAGACTTGGAACCCAATGTGGTCTGTTTCAAG                         TATTTTGACTGGCCTTCTGTCTTTTATG
genomic: TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgt ... tttgatgcagTATTTTGACTGGCCTTCTGTCTTTTATG
EST: gi|208368770|gb|DC951336.1|DC951336
EST:     TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG                         TATTTTGACTGGCCTTCTGTCTTTTATG
genomic: TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgt ... tttgatgcagTATTTTGACTGGCCTTCTGTCTTTTATG
EST: gi|208365980|gb|DC955499.1|DC955499
EST:     TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG                         TATTTTGACTGGCCTTCTGTCTTTTATG
genomic: TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgt ... tttgatgcagTATTTTGACTGGCCTTCTGTCTTTTATG

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), 9 (downstream exon)
Score: 1

TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAGgtatttttgt ... tttgatgcagTATTTTGACTGGCCTTCTGTCTTTTATG




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