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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA

Basic information

species Physcomitrella patens
transcript PP1S99_260V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 14
ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgc-cagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA
          ||| |      ||    |   |  ||    |||  | ||   |  | ||| |  ||      || |||| | | |    |  |  |  ||||| || |||||||| ||| | ||||| |||||||| || ||||| ||||||  | | || || ||||||||||||||||| ||||| ||||||||||| |
----------gtgcacctg--cagtttttatgctataacgatc-aatattaactat-tggaggctacttttccttacctgttgttatttttcttcgtgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
ttagccccatgtgaattaaaacaaa--aatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtat---gccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA
 ||           ||||  ||| |  ||| || ||     | |    | | ||     | |      ||   | | | |||   ||   ||  |     | ||||| || |||||||| ||| | ||||| ||||| || || ||||| ||||||  | | || |||||||||||||||||||||||||| |||||||||||||
gtatttgttcagttattatcacagactaattga-tagccattttggtgattttgtaccatcgaaaactaatggttttatcttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 13
-----ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA
     | ||   ||  |  || |   ||| ||| |  | ||||   |    |||   |  ||   |   |||  |  ||||   |||       |    |  |||||| |||| ||||| || || |||||||| |||||||||||| | ||||||  | | |||||||| ||||| |||||||| ||||| |||||||| ||||
ttacatgagttacacatacat-atttcaataattgtattattctagtaattaataaacactgcctt---taatcctactgaatgttgt-cattgtaactttgcagTTTGTATTTTCAACTGCCATTGATGGCAAAATAAAAGCCTGGTTATATGATAATATGGGTTCTAGGGTTGATTATGATGCCCCAGGTCATTGGTGTACTA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 14
----ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA
    | ||   |  ||  ||     | | ||| |  | ||||   |    |||   |  ||       | || | |   |  | | |      |  | |  |||||| |||| ||||| || || |||||||| |||||||||||| | || |||  | | |||||||| ||||| |||||||| ||||| |||||||| ||||
tacatgagttacgagtacatattgtcgataattgtattattctagtaattaataaacactgc----ctttaatcttactaaatgttgtcattgtaattttgcagTTTGTATTTTCAACTGCCATTGATGGCAAAATAAAAGCCTGGTTATACGATAATATGGGTTCTAGGGTTGATTATGATGCCCCAGGTCATTGGTGTACTA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 12
-------------------------------------------------ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgt-gcggtgtggtgtgta-aaacctctgacctttg----gatg-acctcgt----------atgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA
                                                 ||   || ||  |  ||  || || |||  ||||      |  |   || | |   | |  ||  ||  ||  ||||  ||||      ||  | |||||          ||  ||||| ||||| ||||| || || ||||| || |||||||||||||| ||||||  ||| ||||| ||||||||||||||||| || ||  | ||||| || |
gtgcggcaaggattgaatcaaactatattttacatcaattattatactgttttaccaatccg--tttgaagaacaataaagtagacgacacatttcatatagtattatcttgcctatgaatttctgttctttaccaaaatacatctcgttcttatttggatttcagTTCATATTTTCAACCGCCATAGATGGGAAAATAAAAGCCTGGCTTTATGATAATCTGGGTTCCAGAGTTGACTATGATGCTCCCGGTAAATGGTGTACGA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 13
--ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA
    || |   | |   |||||| | |  || |  | ||    | |        || |||  |||     |  | |  | |||        |  ||||| |||||||||||||||| ||| | ||||| ||||| || || ||||||||||||  | |||||||| | ||||| ||||| ||||| || || ||||| || |
gtgcaggcatctcttgtttaaaa-agacctgaaaaactttcccttt--------cgctgtcttgtaatttatttttctctttt------tttactatgc-agTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 14
-ttagccccatgtgaattaaaacaaaaatggagtaattcgtatctgaaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA
 || |      |||  ||     || ||      || | |  | |   || ||  | ||  ||| |||||  |    ||||         |   || ||||||||||||||||||||| || ||||| || ||||| || ||| | ||||||    | || ||||||||||| ||||||||||| || ||||  |  || |
ttttgtatttggtgctttgcgttaagaacaactgaactagattttatcatatggtg-gttatgtttaaaaatttcccccttatttctggtttccatcccagTTTATATTCTCAACAGCAATTGATGGGAAAATAAAGGCATGGTTGTATGATAACATGGGCTCTAGAGTTGATTATGATGCACCGGGTCATTCATCTACAA

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: 29 (upstream exon), 30 (downstream exon)
Score: 13

GTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAGgtgggacatt ... cgtatgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtgcggtgtggtgtgtaaaacctctgacctttggatgacctcgtatgccagTTTATATTCTCAACAGCTATCGATGGCAAGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTA
                         ctctgac  putative branch site (score: 13)
                 tgtaaaa  TA-rich tract