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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagtgcatttggactaagaattagatgagtttattaccactacgttcatacacaagtcaatttcacactaagattaacgtctttctcccatatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG

Basic information

species Physcomitrella patens
transcript PP1S131_16V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 7
gaagtgcatttggactaagaattagatgagtttattaccactacgtt-catacacaagtcaatttcacactaag-attaacgtctttctcccatatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG
        | ||   ||    | |  ||| ||| |    | ||  || | ||     |      |||   ||   | |  | |   | |        |  |||||||   ||||||||| ||||||| ||   |||||| ||||||||||||||||||||||| ||| |
-------gtatgatttagttgtcaactgattttttattaattatatttcgtattttggcagtactcaatttactcacttcctttgctattttgggcttacagCTACTAAGTGGAGGGATAGTACAACAGGCTCGCATGTGGAATATGACCAAAGGCCTGATGTTTTCAG

upper sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA07G01890.1 (Glycine max), 3'ss of exon 7
gaagtgcatttggactaagaattagatgagtttattaccactacgttcatacacaagtcaatttcacactaagattaacgtctttctcccatatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG
   ||    ||    |   || ||  |   ||||||     ||  ||| ||     |      |||       | |  | |   | |        |  |||||||   ||||||||| ||||||| ||   |||||| ||||||||||||||||| ||||| ||| |
---gtatgatttagttgtcaactaattt--tttatttattatattttcgtattttggaagtactcatttactcacttcctttgctattttgggcttacagCTACTAAGTGGAGGGATAGTACAACGGGCTCGCATGTGGAATATGACCAAAGGCCAGATGTTTTCAG
















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|162252531|gb|FC427340.1|FC427340
EST:     ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTG                         CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
genomic: ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTGgtgagttttc ... atatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
EST: gi|162228110|gb|FC405692.1|FC405692
EST:     ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTG                         CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
genomic: ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTGgtgagttttc ... atatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
EST: gi|162257792|gb|FC433990.1|FC433990
EST:     ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTG                         CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
genomic: ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTGgtgagttttc ... atatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
EST: gi|162163687|gb|FC340286.1|FC340286
EST:     ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTG                         CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
genomic: ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTGgtgagttttc ... atatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
EST: gi|162257871|gb|FC434069.1|FC434069
EST:     ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTG                         CTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA
genomic: ACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTGgtgagttttc ... atatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAA

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: 35 (upstream exon), 34 (downstream exon)
Score: 15

GTATGTACATGGAGACGTGAAGCCCGAGAACTTCCTCCTGGGACAACCTAATACACCTGACGAGAAGAAGCTTTTTCTTGTAGATCTCGGGCTTGgtgagttttc ... atatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatacacaagtcaatttcacactaagattaacgtctttctcccatatgtgaagCTACTCGATGGAGGGATGGTACAACCGGTCAGCATGTAGAATATGACCAAAGGCCTGATGTGTTCCG
                           gattaac  putative branch site (score: 15)
                                 cgtctttctcccat  CT-rich tract
                        taagattaa  TA-rich tract