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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatttaagctgccaacgaggtagttagaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA

Basic information

species Physcomitrella patens
transcript PP1S316_34V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 14
cttatttaagctgccaacgaggtagtta-gaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
           |||    |  ||  ||| |  ||     || || |  |||  |||| |    |     ||| |  |  | | | |   || |   | ||||| || |||||||| ||| | ||||| |||||||| |||||||| ||||||    | ||||| ||||||||||| ||||| || || ||||||||||| |
----------gtgcacctgcagtttttatgctataacgatcaatattaact--attggaggctacttttccttacctgttgttatttttcttcg--tgcagTTCATCTTCTCAACTGCTTTGGATGGAAAGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G030422_T02 (Zea mays), 3'ss of exon 14
--cttatttaagctgcca--acgaggtagtt-agaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
   ||  || || |   |  ||    || || | |    |  |  |   | |    ||| | | |  |   |   ||   || ||  | |    | |    |||||| || |||||||| ||| | ||||| ||||| || || ||||| ||||||    | ||||||||||||||||| |||||||| ||||||||||||||||
gtatttgttcagttattatcacagactaattgatagccattttggtgattttgtaccatcgaaaactaatggttttatc-ttattatattcttattcttggtcagTTCATCTTCTCAACTGCTTTAGATGGGAAGATCAAGGCATGGCTATATGATAATTTGGGATCTAGAGTTGACTATGATGCACCAGGTCATTGGTGCACTA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 14
cttatttaagctgccaacgaggtagttagaaatgt---gcttctatctgtactgc--attgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
  |  ||   ||| |   ||  ||  || | || |   | ||  ||    | |    |||||     |  |     ||   ||||  |||    |     | ||||| || |||||||| || | |||||| || |||||||| ||| | ||||||  | | || ||||| |||||||| ||||||||||||||||  |  ||||
--ttgttggactggccttgatatatatatatatatattgttttgattcacattttcgattgtgttataaaattttcaactgtgttctaata---tggctctgcagTTCATCTTCTCAACTGCAACTGATGGAAAAATAAAAGCATGGTTGTATGATAACATGGGTTCTAGGGTTGACTATGATGCACCTGGTCATTCTTCTACTA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA17G12110.1 (Glycine max), 3'ss of exon 14
-cttatttaagctgccaacgaggtagttagaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
   |  |     |     |    |  |    | | || ||  ||    | |      |     || |    |  || ||| |   ||   |     | ||||| || |||||||| || | |||||| || |||||||| ||| | ||||||  | | || ||||| |||||||| ||||||||||||||||  |  ||||
atgtggtggtcatattttcacattgttggatagtttgttttgattcacattttcgattgtgttataaaattttcaactgtgttc-tgatatggctctgcagTTCATCTTCTCAACCGCAACTGATGGAAAAATAAAAGCATGGTTGTATGATAACATGGGTTCTAGGGTTGACTATGATGCACCTGGTCATTCTTCTACTA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 13
cttatttaagctgccaacgaggtagttagaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
         || | || |    | |||  ||| |  ||   |    | |    | |     | ||     ||   || | |   |    ||| ||  ||||||||||||||||| ||| ||||||| ||||| || || ||||||||||||    |||| ||| | ||||| || || ||||| || || ||||| || |
-------gtgcaggcatctc--ttgtttaaaaagacctgaaaaactttccctttcgc-tgtcttgtaatttatttttctct---ttttttactatg-cagTTTATATTCTCAACCGCTCTTGATGGAAAGATCAAGGCGTGGCTCTATGATAATGTTGGTTCTCGGGTTGATTATGACGCACCGGGACAGTGGTGTACAA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 14
-cttatttaagctgccaacgaggtagttagaaatgtgcttctatctgtactgcattgtaca-gcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
  || | |  | |||    | | ||   | || ||  ||    | | |  |    ||   | |  | |    |       | |   |||  | || |  |||||||||||||||||||| |||||||| || ||||| || ||| | ||||||  | | || ||||||||||| || |||||||| |||||||  |  || |
ttttgtatttggtgctt-tgcgttaagaacaactgaactagattttatcatatggtggttatgtttaaaaatttcccccttatttctggtttcca-tcccagTTTATATTCTCAACAGCAATTGATGGGAAAATAAAGGCATGGTTGTATGATAACATGGGCTCTAGAGTTGATTATGATGCACCGGGTCATTCATCTACAA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv16s0039g02410.t01 (Vitis vinifera), 3'ss of exon 13
cttatttaagctgc-caacgaggtagttagaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttc---------agTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
         |  ||  ||   |||  |  |||||| | |  |    |   |  || |||   ||| |  || ||  |  |||      |  ||  || |         ||||||| || || || || || ||||| ||||| ||||||||||| ||||||  | | ||||||||||| ||||| ||||| ||||| |||||||| || |
---------gtagcataatatggtcttaggaaatgggatattgcaagggttatatggtatt-catcatgcccaatttcatttatccaactcacttttcctttgtctgcagTTTATTTTTTCTACTGCCATAGATGGGAAGATTAAAGCTTGGCTATATGATTGCTTGGGATCTAGAGTAGACTATGATGCTCCTGGACATTGGTGTACCA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv09s0002g07020.t01 (Vitis vinifera), 3'ss of exon 13
cttatttaagctgccaacgaggtagttagaaatgtgcttctatctgt-actgcattgtacagcatgagccctaaaattgtttga-atggcctacaat--ttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
    |  ||  |    | | |  |  ||    ||||    ||    | |   ||   |     ||  |   | ||||   |  | |||  || |  |  ||||||| || || ||||||||||| ||||| ||||| || || ||| | ||||||  | | || || |||||||||||||||||||| |||||||  ||||| |
----tgaaaatttgagaagtgtaaaatatgtttgtgtccttagacattatcccaaactctcaaatatggtttcaaatcactaaagatgttcttctctcgttcagTTCATCTTTTCAACAGCTATAGATGGAAAGATTAAGGCATGGTTATATGATAACTTGGGTTCAAGAGTTGACTACGATGCACCAGGTCATTCCTGCACAA

upper sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 13
------------cttatttaagctgccaacgaggtagttagaaatgtgcttctatctgta-ctgcattgtacag-----catgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
             |   ||  |||       || | || |    | | |  ||  ||||| || | || | | |     | |  | ||| |  || | |   ||   |     |||||||||| || ||||||||  ||||||| ||||||||||| ||| | ||||||  | | |||||| ||||||| || ||||| || ||||  |||||||| |
gtaacaagtccattagctttggctattc-taagtttgtcatgttttttcgccttcctgtaactactttcttctgtcatcccttggtcctgatgttctgtttgtgcttttatgcttcagTTTATCTTTTCAACAGCACTTGATGGGAAGATAAAAGCATGGTTATATGATAACTTGGGATCTCGAGTTGATTATGATGCTCCAGGTCGCTGGTGCACAA

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: 32 (upstream exon), 30 (downstream exon)
Score: 11

GTTTGGGATGCTGCAACAGGACGTAAGCAATACACTTTTGAAGGACATGAAGCACCTGTGTACTCTGTTTGTCCTCATCATAAAGAGAGTATTCAGgttggatttt ... acaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA
                      ccctaaa  putative branch site (score: 11)
                         taaaattgtttgaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttatttaagctgccaacgaggtagttagaaatgtgcttctatctgtactgcattgtacagcatgagccctaaaattgtttgaatggcctacaatttcagTTTATATTCTCAACAGCTATTGATGGCAAGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTA

- - - - - - - - - - - - - - - - - - - - - - - tactgca