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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttgggggattccacggtcttatatttcccatggcgacctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA

Basic information

species Physcomitrella patens
transcript PP1S104_2V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os07g06950.1 (Oryza sativa), 3'ss of exon 6
gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttgggggattccacggtcttatatttcccatggcgacctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
               || ||| ||  |   |  |  |||  ||| |       || |   |||     |    |  | |   |    ||  |  || |||| || |||||||| |||  |||||||||||||||||||||||| || || || |||||  |   |||  | ||  | |     | ||| | ||| || ||
--------------gtgcattcatcatc-tatgcctttttctttat-------ttagtcaattgggttgcgaaaagtattttaatctgaaattctttcagAAACACAACATCAATTCTCTGCTCGAGAAAGTGATTGGGGTTTTACTTCCTTTATGCCTTTGGGTGATCTCTACAACCCCAGTAGAGGCTATCTTGTAAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 4
------gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttgggggattccacggtcttatatttcccatggcgacctatttg-cagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
        ||| | |  ||||| | | |||      |||  ||        |  |    || |  |   | |  | |||  |  |    ||   || | |||| |||||||||||||||| || ||||| || || ||||| ||||||||||| || || |||||  |   |||  | ||||| | |   |  || |  || || ||
tggatattgagaacttctaattttttctatacgtggaaataatgaaagcctt--ttgtattagcag---cgattgacttgcacatgt--tgcttacatgtttggcagATACTCAACATCAATTTAATGCACGTGAGAGTGACTGGGGTTTCACATCTTTTATGCCTTTGAGTGATCTGTATGACCCAAGTAGGGGCTACCTTGTTAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G018508_T03 (Zea mays), 3'ss of exon 1
gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttggg---ggattccacggtcttatatttc---------ccatggcg----acctat-----ttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
  |   ||||||  || | ||     ||     | |  | |    ||   || |   |   || |||||   | | |  |||          |   ||||    || |||     ||||||| || ||||||||||||  ||||||||||||||||||||||||||| ||||| |||||  |   |||  | ||  | |     | ||||| ||| || ||
--gtccattctt--ttatcttgcccttgtttttcaacctagcacatgtcaagatattgattggcttccatactttgaggttttagtgacaaacttaggcgtctgacttataattcttgcagAAACACAACATCAGTTCTCTGCTCGAGAAAGTGATTGGGGTTTCACTTCATTTATGCCGTTGGGTGAACTCTACAACCACAGTAGAGGTTATCTTGTAAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G864266_T01 (Zea mays), 3'ss of exon 4
------------------gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttgggggatt--ccacggtcttatatttcccatggcgacctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
                       | || | ||        |||   | | |  | |||| || |    |  ||||||  |   | ||   ||||  | || ||     |  |  ||||||| || ||||||||||||  ||||||||||||||||||||||||||| ||||| ||||| ||   |||  | ||  | | |   |  |||| ||| || ||
gtccatccgtttatcacgcccttgtttttcaacctagcacattccaagatatcaattggattctat--actttggggtttcagcaacaaacttaggtgtctcacttttaatt-cttgcagAAACACAACATCAGTTCTCTGCTCGAGAAAGTGATTGGGGTTTCACTTCATTTATGCCGCTGGGTGAACTCTACAACCCAAGTAGGGGTTATCTTGTAAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 4
gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttgggggatt-ccacg-gtcttatatttcccatggcgacctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
            ||  | | | |  | |  | |  ||     |  |  | |  || ||| ||  ||| | |  || |  |  |         |  | || ||| || || || || |||||||| || |||||||||||||||||||| || |||||||||||   ||| || |||||||     | ||| | ||| |||||
--tttaccatgaaacagaagtaacaggggaataaaatgaaaatgctcataatttttgggcatagccatgtgctttgtcataacttcattttacactatgtagACACACAGCACCAATTCAATGCGCGGGAAAGTGATTGGGGTTTCACGTCTTTCATGCCACTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 4
gagaggattcttaattgtatttattgtgacaaacgatttggtttg-tggtgaggttgggggatt-ccacg-gtcttatatttcccatggcgacctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
      |   | ||    |  |     |  ||   | | |   || |  | |  || ||| ||  ||| | |  || |  |  |            | || ||| || || || || |||||||| || |||||||||||||||||||| || |||||||| ||   ||| || |||||||     | ||| | ||| |||||
---tttaccatgaaacagaagtgacaggggaataaagtggaaatgctcataatttttgggcatagccatgtgctttgtcataacttcattttatgctatgtagACACACAGCACCAATTCAATGCGCGGGAAAGTGATTGGGGTTTCACATCTTTCATGCCGCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 4
gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttgggggat-tccacggtctta-tatttcccatggcgaccta---tttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
  ||  ||| ||  || |||| |  | |  ||  ||    ||      |    || ||   | || | |  |||  |    |  |     |  ||   | |||||| || || || ||||| ||||| || |||||||||||||||||||| || |||||||| ||   ||| || |||||||     | ||| | ||| ||| |
--gattatttttttttttattaaaagagg-aagtgaa--agtgcacaattctttttggatttatctatgaccttggtcaagcttaattttatttatactatgcagACACACAGCACCAGTTTAATGCACGTGAAAGTGATTGGGGTTTCACATCCTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGCA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 4
gagaggattcttaattgtatttattg--tgacaaacgatttg---gtttgtggtgaggttgggggat-tccacggtctta-tatttcccatggcgaccta---tttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
          | |||| ||||| ||   | | | | ||  ||   ||      |    || ||   | || | |  |||  | |  |  |     |  ||   | |||||| || || || ||||| ||||| || |||||||||||||||||||| || |||||||| ||   ||| || |||||||     | ||| | ||| |||||
----------tcaattatatttttttattaaaagaggaagtgaaagtgcacaatttattttggatttatctatgaccttggtgtagcttaattttatttacactatgcagACACACAGCACCAGTTTAATGCACGCGAAAGTGATTGGGGTTTCACATCTTTCATGCCTCTTGGTGAATTGTATGATCCTAGTAGAGGGTATCTTGTGAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G06600.1 (Arabidopsis thaliana), 3'ss of exon 4
---gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttgggggattccacggtcttatatttcccatggcgacctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
    |   | ||  |    | | ||  | | |  |   |  | | |    ||||  |||| | || |      || | |||     |    ||    ||||||| || |||||||| ||||||||| ||||||| |||||||| || || ||||||||||||||    ||  | |||||||     | ||| | | | |||||
atttacctggtttctggc-gaacttggtattatcag-aacctagctgtaagtgaccttggtg-atacaggtcactgacattatgattcctaactgtgttgcagAGACGCAACATCAATTCAATGCTAGAGAAAGCGATTGGGGATTTACATCATTCATGCCACTTAGCGAACTTTATGATCCTAGTAGAGGATATTTAGTGAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 4
gagaggattcttaattgtatttattgtgacaaacgatttgg-tttgtggtgaggttgggggattccacggtcttatatttcccatggcgacctattt---gcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
 | |  || ||  ||| |||||    |   |||| || |   ||| || |||  |||     || ||  |  ||     |   |   |    |   |   |||||||| ||||| ||||||||||| || |||||||||||||| ||||| ||||||||||| ||   |||  | ||||| |   | | ||||| ||| |||||
tatataatgct--attttattttacctataaaacaatgtaactttctgatga--ttgatcattttcaatgctttgatgatttaaaatccttatgcctgcggcagATACACAACACCAGTTCAATGCACGTGAAAGTGATTGGGGATTCACTTCATTCATGCCTCTTGGTGAACTGTATGACCCTGCAAGAGGTTATCTTGTGAA

upper sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 4
--gagaggattcttaattgtatttattgtgacaaacgatttggtttgtggtgaggttgggggattccacggtcttatatttcccatgg--cgacctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
   ||| | || ||  || |  ||||| || |||| ||  ||  | || | ||  |||||    |  |   | || |  |  | ||    |   |  | |||||| |||||||| ||||| ||||| ||||||||||||||||||||||| || || ||||| ||   |||  |||| |||| |   |  |||||||| |||| 
tgaagatggttgttttttatccttatt-tgccaaa-gacatgtatagttg-gatattgggtttattta-aattttgtgatggctatctttcttgcattctgcagACACTCAACACCAGTTTAATGCACGAGAAAGTGATTGGGGTTTCACTTCTTTTATGCCTCTTAGTGAACTATACGATCCAGGTAGGGGTTTTCTTGTGAG

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: 17 (upstream exon), 32 (downstream exon)
Score: 2

GTTGCTGACTCGAACCAACTGCCGAGTGGCTGGACCAGATTTGCACATTTTAACTTGGCTGTTCTTAATCAATATGAACCCAAGATGTCTGTTCGGAAAGgtttggcgtt ... ctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgaggttgggggattccacggtcttatatttcccatggcgacctatttgcagATACTCAACATCAGTTCAATGCTCGAGAAAGTGATTGGGGTTTCACCTCATTCATGCCACTACATGAGTTATATGATCTATCGAAAGGTTTTCTGGTGAA
                                            cctattt  CT-rich tract
                        tcttatattt  TA-rich tract