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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttccttatcgtacttgtcaacatggaactcagcgctagcatatgaacttataaaaaatatgacgcaacgaaaactttattgttgtgcttttcttacagGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG

Basic information

species Physcomitrella patens
transcript PP1S203_55V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G13680.1 (Glycine max), 3'ss of exon 3
ggttccttatcgtacttgt-caacatggaactcagcgctagcatatgaacttataaaaaata-tgacgcaacgaaaactttattgttgtgcttttcttac-agGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG
      | |    | |    || | | |   |  | | ||   | | |  || ||     |  |  |  || | ||  ||| || || |    ||   || |||||||  | || ||    || |||||  |    |||||||| ||||| |||||||||||||||||| | || || ||    | | |||||||
-----gtgagaaaattcaagcatccttgttttttgagttattgtctaatgttgtagttttttcttccataatgtaatttttttttttttttggtttcaaccagGGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACG

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G30530.1 (Glycine max), 3'ss of exon 3
----ggttccttatcgtacttgtcaacatggaactcagcgctagcatatgaacttataaaaaatatgacgcaacgaaaac-tttattgttgtgcttttcttacagGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG
    |     | |  | |   ||     | ||  |     |||   |   |  ||         || | | |         ||| ||  | |   ||||  |||||||||  |||| ||    || |||||  |    |||||||| ||||| |||||||||||||||||| | ||||| |     | | |||||||
gtgagaaaattaaaagcatacgtgttttttgagttattgtctactgttgtagttttattcttccataatgtattttttttgtttgtttgttttggtttcaaacagGGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACG

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G21100.1 (Arabidopsis thaliana), 3'ss of exon 3
ggttccttatcgtacttgtcaacatggaactcagcgctagcatatgaacttataaaaaatatgacgcaacgaaaactttattgttgtgcttttcttacagGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG
      | |   || || ||   || |||  |    ||    | |||     ||| |  || |   ||| |  || || || |   | | | | || ||||||||  |||||||| |  | ||| |  |    |||||||||||||| ||||||||||||||||||   ||  ||      | ||||||| |
-----gtgagtatagttttct-tattgaatacttttctc-tgtctgag---gtaatacgtaagtaacaatgttaa-ttgatagcacttcatcttttgcagGGTGAAGCACAAGACTTTTTGTTTGTTGCAACTGAAAGATATAAATTCTGTGTTCTTCAATGGGATTATGAGTCCTCTGAGCTTATTACAAG

upper sequence: PP1S203_55V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 3'ss of exon 3
---ggttccttatcgt-acttgtcaacatggaactcagcgctagcatatgaacttataaaaaatatgacgcaacgaaaactttattgttgtgcttttcttacagGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG
    ||  | | | || || | |  | |    ||| ||   |||||| |  | | ||      ||||     || |   |||   |||| ||  || || |||||| ||  |||||||  | ||||| ||  |    |||||||| || |||||||||||||||||||||||||| |          ||||||| |
gtaagtatcatcttgtgacatatagaaagcttacttag---tagcat-tataatcatgctttttatgctaatactattgctt-gctgttttggatt-ctaacagGGCGAAGCACAAGATTTTCTATTCATCGCAACTGAAAGATACAAGTTTTGTGTTCTTCAATGGGATGCAGAGAATTCTGAGGTTATTACAAG

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: 23 (upstream exon), 20 (downstream exon)
Score: 2

TCTATGCTCGATGTCCCTTTGTATGGCAGAATCGCCACACTGGAGCTCTTTCGCCCTCCTgtaagttact ... tttcttacagGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacttataaaaaatatgacgcaacgaaaactttattgttgtgcttttcttacagGGTGAGTCACAAGACGTGCTATTTATATCGTTCGAAAGATATAAATTTTGTGTTCTTCAATGGGATGCAGAAACCGGCTCACCTATTACACG
                                         tgcttttctt  CT-rich tract
     tataaaaaatatga  TA-rich tract