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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTGGTGAAGTACTCGTCCACCAAATGATTCACACCATTGAGTTTGTGTTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgccatgtttgtgataatggctttcgtcaatgcagagtaattatttggtgccggtttttaaagttctgatgatatggtttttcacattttgaagttttgcacttggtctttgtgtatgcag

Basic information

species Physcomitrella patens
transcript PP1S6_159V6.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S6_159V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 5'ss of exon 16
AGTTTGGTGAAGTACTCGTCCACCAAATGATTCACACCATTGAGTTTGTGTTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtac------ttgccatgtttgtgataatggctttcgtcaa-tgcagagtaattatttgg----tgccggtttttaaagt--tctgatgatatggtttttcacattttgaagttttgcacttggtctttgtgtatgcag-----------------------------------------------------
| ||  | ||| |  | || |||||| | ||||||||||||||||||||| | || || || |||||||||||||||||||| || ||||||||  | ||||||       | |    |||   ||| |     | ||||  | |    || |  |        |  |  || | ||  |  |||     ||   || |    | ||    | ||     | | |   |||  | | |                                                      
AATTCAGCGAAATCTTTGTGCACCAACTCATTCACACCATTGAGTTTGTGCTTGGAGCTGTTTCCAACACTGCTTCTTATCTTCGTCTCTGGGCTCTCAGgtacaaaatactacttgctttcaaatagtcctgattgtcatctaccagatagtcctaccaaaactagcacttgtcaatatcatctagcagtagtattctgttaaattcattggttcttgatggcttaatgtcgaagtattggtttgcgcatttcgtgactaatctttatgctttgctgggattcctattcag

upper sequence: PP1S6_159V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 5'ss of exon 16
AGTTTGGTGAAGTACTCGTCCACCAAATGATTCACACCATTGAGTTTGTGTTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgccatgtttgtgata-atggctttcgtcaatgcagagtaattatttggtgccggtttttaaagttctgatgatatggtttttcacattttgaagttttgcacttggtctttgtgtatgcag
| ||  | ||  || | || || ||  ||||||||||||| ||||||||| | || || || |||||||| |||||||| ||||| || |||||  | |||||   |   |    |  ||| |||  || | | ||   | | |  |   ||  |  |  || ||    ||| |                                                     
AATTCAGCGAGATATTTGTGCATCAGCTGATTCACACCATAGAGTTTGTGCTTGGAGCTGTTTCCAACACCGCTTCTTACCTGCGTCTATGGGCTCTCAGgtatgagtagtagaagctatacatgaattacat-aacctatactcgtggcttaatatccattcttttgtttcag-----------------------------------------------------

upper sequence: PP1S6_159V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: EFJ28428 (Selaginella moellendorffii), 5'ss of exon 15
AGTTTGGTGAAGTACTCGTCCACCAAATGATTCACACCATTGAGTTTGTGTTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgccatgtttgtgataatggctttcgtcaatgcagagtaattatttggtgccggtttttaaagttctgatgatatggtttttcacattttgaagttttgcacttggtctttgtgtatgcag
| ||||||||     ||||||||||||||||  | ||||||||||| ||| | ||||| ||||| ||||| ||||| ||||| || || |||||  | |||||    |||  |||||  |  |   ||||||         ||  |||  |     | |                                                                   
ACTTTGGTGAGACCTTCGTCCACCAAATGATAGAAACCATTGAGTTCGTGCTAGGTGCTGTGTCGAACACAGCTTCCTATCTCCGGCTGTGGGCTCTCAGgta--aaccaactttgttttcgtttgtttcgtgctcctgacgtgtttagctttccacag-------------------------------------------------------------------

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|162174813|gb|FC352229.1|FC352229
EST:     TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAG                         CCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
genomic: TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
EST: gi|162152879|gb|FC328973.1|FC328973
EST:     TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAG                         CCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
genomic: TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
EST: gi|37849887|gb|BJ607895.1|BJ607895
EST:     TGGGCATTGAG                         CCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
genomic: TGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
EST: gi|162189972|gb|FC365623.1|FC365623
EST:     TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAG                         CCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
genomic: TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
EST: gi|162156042|gb|FC332209.1|FC332209
EST:     TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAG                         CCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
genomic: TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
EST: gi|162156984|gb|FC333346.1|FC333346
EST:     GACTCTGGGCATTGAG                         CCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
genomic: GACTCTGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
EST: gi|162173249|gb|FC350031.1|FC350031
EST:     TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAG                         CCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
genomic: TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
EST: gi|208368650|gb|DC940029.1|DC940029
EST:     TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAG                         CCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT
genomic: TTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTT

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: 4

AGTTTGGTGAAGTACTCGTCCACCAAATGATTCACACCATTGAGTTTGTGTTGGGTGCCGTGTCCAACACTGCTTCTTATCTGCGACTCTGGGCATTGAGgtacttgcca ... gtgtatgcagCCTTGCACACGCACAACTTTCTGCGGTGTTCTATGAGCGAGTCCTCATGTTTGCTTGGGC




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