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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgaccaccttatgacatcgcatttccatgccttgccatctgctccgatatgtgactttggaggtctgactacatcgtatgaatttcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA

Basic information

species Physcomitrella patens
transcript PP1S73_26V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G151549_T02 (Zea mays), 3'ss of exon 1
atcgaccaccttatgacatcgcatttccatgccttgccatctgctccgatatgtgactttggaggtctgactacatcgtatgaa--tttcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA
  | |    |  |||| |        |  ||| ||      ||||      |||    |   |  |   | |  || |    |   ||  ||  |  || |||||||| |||| || ||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| ||  |||| ||||| || ||||||||  
--caaaattcagatgaaacgttgaagctgtgcattttttattgctatagcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG

upper sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G132144_T01 (Zea mays), 3'ss of exon 5
atcgaccaccttatgacatcgcatttccatgccttgccatctgctccgatatgtgactttggaggtctgactacatcgtatgaa--tttcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA
 || |    |  |||| |        |   || ||   || ||||      |||    |   |  |   | |  || |    |   ||  ||  |  || |||||||| |||| || ||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| ||  |||| ||||| || ||||||||  
-tcaaaattcagatgaaacgttgaagctgcgcatttttat-tgctatagcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATCGTG

upper sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G107893_T01 (Zea mays), 3'ss of exon 4
atcgaccaccttatgacatcgcatttccatgccttgccatctgctccgatatgtgactttggaggtctgactacatcgtatgaa--tttcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA
 || |    |  |||  |        |  ||| ||   || ||||      |||    |   |  |   | |  || |    |   ||  ||  |  || |||||||| |||| || ||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| ||  |||| ||||| || |||||| |  
-tcaaaattcagatggaacgttgaagctgtgcatttttat-tgctatagcttgttttgtgataattgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG

upper sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G038028_T01 (Zea mays), 3'ss of exon 6
atcgaccaccttatgacatcgcatttccatgccttgccatctgctccgatatgtgactttggaggtctgactacatcgtatgaa--tttcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA
 || |    |  |||| |        |  ||| ||   || ||||      |||    |   |  |   | |  || |    |   ||  ||  |  || |||||||| |||| || ||||| ||||| || |||||||| || || |||||||||||||| ||||| ||||| ||  |||| ||||| || |||||| |  
-tcaaaattcagatgaaacgttgaagctgtgcatttttat-tgctatagcttgttttgtgataaatgctaatgaattgatcaatccttgtttaccaatgcagATCGGTCCTGACCAGATTGAAGCTCTGTATCAGTATGCCAAATTTCAGTTTGAGTGTGGTAACTACTCAGGGGCTGCTGATTACCTTTACCAGTATGGTG

upper sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 2
----atcgaccaccttatgacatcgcatttccatgccttgccatctg--ctccgatatgtgactttggaggtctgactacatcgtatgaatttcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA
     |        |||  | |      ||| |    | |   | ||   |  |   | ||| |   |   ||||||||  |         |||| ||      |||| ||| |||  || || || ||  | ||||| ||||| || ||||||||||||||||||||||| || |||||  ||||||| || ||||||||  |  
ctgttttagtggttttaaaaga--attattctacttttggaagtttgaattttgtggtatgagtcctg---tctgactatgtaaacaatgattctgctgaa-acagATTGGTCCTGCACAGATAGAAGCGTTGTACCAATATGCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAGTACAGAG

upper sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G33770.1 (Glycine max), 3'ss of exon 2
atcgaccaccttatgacatcgcatttccatgccttgccatctgctccgatatgtgactttggaggt--ctgactacatcgtatgaatt----tcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA
        |  |||   |  |  |||  | |  |   | |    |     |  ||| ||| | |||   ||| | ||  || | |||     |  |    |   |||| ||| |||  || || || ||  | ||||| ||| | || ||||||||||||||||||||||| || |||||  ||||||| || ||||| ||  |  
------tgctgtattttagaggttttaaaagaatcatcctagttttgagaagttgaattttgtggtatttgagttcactgtgtaaatgaggattctgctgtaacagATTGGTCCTGCACAGATCGAAGCATTGTACCAATATTCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAATACAGAG

upper sequence: PP1S73_26V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 2
atcgaccaccttatgacatcgcatttcca-tgccttgccatctgctccgatatgtgactttggaggtctgactacatcgtatgaatttcttctcttt---gtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA
     ||   || ||   | | |||     |   ||| ||        | | | ||  | |    | || || | ||  |||   ||| |||| ||      |||| ||    || || || |||||  | || |||||||| || || |||||||| ||||||||||| || |||||  |||| ||||| ||||||||  |  
----tcctgtttttgttgttgtattgttgctaatttgacagaattctaggtttttgggtctatttggcttacaaaattatatcccttttttcttttctgaccagATTGGCCAGGAGCAGATAGAGGCATTATATCAGTATGCCAAATTTCAGTTTGAATGTGGAAACTACTCTGGTGCTGCTGATTACCTGTATCAGTACAGGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18375480|gb|BJ207058.1|BJ207058
EST:     TGCGATCTGATCAGCAGTACAATTTGCAGATGTTACAGGAACGGTACCAG                         ATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTT
genomic: TGCGATCTGATCAGCAGTACAATTTGCAGATGTTACAGGAACGGTACCAGgttagctcca ... ctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTT
EST: gi|18346243|gb|BJ178286.1|BJ178286
EST:     TGCGATCTGATCAGCAGTACAATTTGCAGATGTTACAGGAACGGTACCAG                         ATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTT
genomic: TGCGATCTGATCAGCAGTACAATTTGCAGATGTTACAGGAACGGTACCAGgttagctcca ... ctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTT
EST: gi|100388025|gb|BY988498.1|BY988498
EST:     TGCGATCTGATCAGCAGTACAATTTGCAGATGTTACAGGAACGGTACCAG                         ATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGT
genomic: TGCGATCTGATCAGCAGTACAATTTGCAGATGTTACAGGAACGGTACCAGgttagctcca ... ctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGT

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: 28 (upstream exon), 8 (downstream exon)
Score: 1

AGCGGCGCCTCTAATCAGCTTCTTACAGAACCCAGCTCTTGTTCAAGAGCTGCGATCTGATCAGCAGTACAATTTGCAGATGTTACAGGAACGGTACCAGgttagctcca ... ctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgatatgtgactttggaggtctgactacatcgtatgaatttcttctctttgtagATCGGTTCTGATCAAATTGAGGCTCTTTACCAGTATGCGAAGTTCCAGTTTGAGTGTGGAAACTATTCAGGTGCCTCTGACTACCTCTATCAGTATCGCA
                   gtctgac  putative branch site (score: 1)
                                       tttcttctctttgt  putative PPT
                                 tatgaattt  TA-rich tract