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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA

Basic information

species Physcomitrella patens
transcript PP1S44_143V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttact--tgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
                                                                                |||||| |     | || ||  | |   ||   |   ||   ||    ||       |  || |  |  ||    |||  || ||| | | ||||||||||||||||  |  |||| || || || || ||||| || || |||||||| |||||||| ||||| ||||| ||||||||||||||  ||||  |
------------------------------------------------------------------------------gtatgcttaa----cccatctcatcagactgcgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtccat-ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

upper sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtat-cttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
                                                                        |||| |||||  | |   ||    | | | | |   |   | ||   |   |   |     |||  |  |||  |   |     |     ||| | | ||||||||||||||||  |  |||| || || || || ||||| || || |||||||| |||||||| ||||| ||||| ||||||||||||||  ||||  |
------------------------------------------------------------------------gtatgcttaacccatctcatcag-actgcgcataaccaaatatgcatatgaaacctg----tgtttgccttgtaacgctgtccat-----ttgatcttcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

upper sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
           ||  | ||  |||||    |    | || |  ||       |  ||     |      | | |||  | ||| ||  |  || | |||||| | | |     ||   | ||  | | ||  |   | ||||          |||||  | ||      ||||||| ||||| || || |||||||||||||| ||  | || ||||| || |||||||| ||||| ||||||||||| || ||  | |||||  | ||| |
----------gtgagtaga-aaatcttgttgccccttttagattttacttcctgttttgcttctc----tgtctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatg--tatgatggtaacaaaatt---------tttgtatcttttat----cagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA

upper sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggac-gcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
                            ||    |||   ||   |   ||     |  |  || | || ||    || |||    |   | || |||  |||    | || | | |        | |  | |  | |    |   |    |  | | | | || ||   ||||||||||||||||  |  |||| ||||| || ||  | |||||||  || ||||| || |||||||||||||||||||||||  | || ||  | ||| |
----------------------------gca-ggttcaaagttagcgttaaaactgttgattcaaaaggctt----ctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtt-tcctcatctctctaacacaatctatgattatttct---cagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA

upper sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ21113 (Selaginella moellendorffii), 3'ss of exon 4
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
                                                                                                                  ||    |  |  |    || ||  |    |   ||||  | |  ||    ||||| ||||||||||||||||||  | || || ||||||||  | ||||| || |||||||| || || || ||||||||||| || |||||||||||| | |||||
------------------------------------------------------------------------------------------------------------------gtaagcttttcatgtctttatgcaagcgagagccttatctttggatt---ctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA

upper sequence: PP1S44_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 4
gtaagatcaaatgtcttgacgaatctgagcgtaattcttcgtcttccacaagtacttaaacacatatggtttgtatcttaatgctttagatttctatttctcctggacgcttgtgtgcagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
                                                                                                                ||  ||  |   |||  | |  ||  |    |   ||||  | |  ||    ||||| ||||||||||||||||||  | || || ||||||||  | ||||| || |||||||| || || || ||||||||||| || |||||||||||| | |||||
----------------------------------------------------------------------------------------------------------------gtaagcttttcatgtc-tttaatgcaagcgagagccttatctttggatt---ctatgtagATGAAAAGATTGCTCTCCTAGGAGCAATCCAATCTCTCTTCGAGGGCTCCATGTACACTTTCGTCTTCCTCTGGACGCCTGCATTGAGTCCTAACGATCA

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: 15 (upstream exon), 25 (downstream exon)
Score: 2

GGCATAATCATGTTGACTTGGCCTGAAAATTATGGCGATCAGGCAGAGGGCAAAAACATCATTGATCAATTTACTAAAGCTGCTGCAGCAATTGCTTCTGgtaagatcaa ... tgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgattgtaatattgtgagaattgggatcttacttgtaaatgttgctatgcagATGAAAAGATTGCTCTTTTGGGTGCTATCCAATCCTTGTTCGAAGGTTCCATGTATACATTTGTTTTCCTCTGGACACCAGCATTGAGTCCTTATGATCA
                            atcttac  putative branch site (score: 2)
     attgtaatatt  TA-rich tract