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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatttaaaatgttacaaaatgagctgctttaagtgcctaaactatctttcagatcttattggtgtttgacccatgaactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA

Basic information

species Physcomitrella patens
transcript PP1S246_34V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 7
agaatttaaaatgttacaaaatgagctgctttaagtgcctaaa-ctatctttcagatctt--attggtgtttgacccatg----aactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
      |    |  | ||     || || |||    || |    |||  |   | || ||  | |  || || ||  |||    |  |||| ||||  |||| | |||||||||||||| |||| |||||  | || ||| | |||||||| |||||||| || |||||||| || || |||||||| ||||| || || || || |
------tgtgtttctgcatgtgcagttggtttcctggcttctttctacatactaaatgtttaagtaatgattaacatatgttaaacttgtttgttc-ttgttggtagTATGAACCAGAGCTGTTTCCAGGACTAATCTATCGCATGAAGCAACCCAAGATAGTCTTGCTTATATTTGTCTCTGGAAAAATTGTTCTGACAGGAGCCA

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 6
--agaatttaaa--atgttacaaaatgagctgctt-taagtgcctaaactatctttcagatcttattggtgtttgacccatgaact-gttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
    | |||||    |||| |    |     |||| |   | | |||   || ||| ||   | ||| |  | ||     |||||| ||| ||||  |||| | ||||||||||||||||||| || ||  | || ||| | |||||||| |||||||| || |||||||| || || |||||||| ||||| || || || ||  
agccattttaagttgtgtttctgctttcctggcttctttctacataataaatgtttaaggaatgattagcatgtgt----tgaacttgtttgttc-ttgttggtaGTATGAACCAGAGTTGTTTCCTGGACTAATCTATCGCATGAAGCAACCCAAGATAGTCTTGCTTATATTTGTCTCTGGAAAAATTGTTCTGACGGGAGCC-

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 7
agaatttaaaatgttacaaaatgagctgctttaagtgcctaaactatctttcagatcttattggtgtt-tgacccatgaactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
      |||    |  |||     |      ||  | | |  |  ||      |   | || ||| |  |||  ||| | || |    ||| || |  ||||| || || ||| | || ||||| ||||||||||| ||||| |  || ||||||||| ||||||| || ||||| |||||||||||  | ||||| || |
-----gtaagtgatctcaagcattgtgatcatatatacttgtaacatg----ggtgttaatcggtctgatgattcat-acctctctcatcattgatgccagTACGAGCCTGAGCTATTTCCAGGATTGATATATAGGATGAAACTTCCAAAGATTGTACTGCTTATTTTTGTGTCAGGAAAGATTGTTATAACTGGAGCCA

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 7
----agaatttaaaatgttacaaaatgagctgctttaa--gtgcctaaactatctttcagatcttattggtgtttgacccatgaactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
      || || ||   ||  ||||  |      | ||   || ||    | |||       ||||||| | ||  |   |       |||| |     |  ||||||||||||||| |||||||| || ||||| ||| ||||||| || || ||||||||  |||||||||| ||||| || || ||||| || ||||| ||||
aaatttaaattgaatcattttaaaaaaaatcatgtaaatgttgtctgtgttctctactgtgccttattg-tattgaatatagt-----ttggattttgttgggcagTATGAACCAGAATTGTTCCCTGGCTTGATCTATCGAATGAAACAACCAAAGATTGTGCTGCTTATCTTTGTGTCAGGGAAAATTGTTCTCACTGGAGCTA

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EDP05450 (Chlamydomonas reinhardtii), 3'ss of exon 4
agaatttaaaatgttacaaa-atgagctgctttaa-gtgcc------taaactatctttcagatcttattggtgtttgacccatgaactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
      |  ||||   | |  | | |||| |        ||       |  || |    || |||   |  |   | |  |||||  || ||| |   |     | |||| || || ||| |||| || ||  | || ||  | ||||||||||||||||||||  |||| ||||||||||| || ||| | || || || |      
-----gtgcaatgcggctagcacgcgctgttgcggcacaccatatggcagcctgttgcccacatcccgtatgccgtggcgccatgc-ctcttgctctgcc--ccgtagTACGAGCCCGAGCTGTTTCCGGGCCTCATCTACCGCATGAAGCAGCCCAAGATTGTGCTGCTGATCTTCGTGTCGGGCAAGGTGGTGCTGACAG------

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 6
agaatttaaaatgttacaaaatgagctgctttaagtgcctaaactatctttcagatcttattggtgtttgacccatgaactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
                 ||   | ||| | ||     |    ||  |||||    |||| |  | || | | |  | || | |||          ||||||| ||||||||| ||||||| || ||||| ||  ||||||||||||| ||||| ||  | || |||||||| |||||||||||||| ||||||||||| |
---------------gtaagtcgtgcttcctttgtcacacttacactcttttc--tcttttgcgggtcttatcactaaagttttg----------tgcagTACGAACCAGAGCTGTTCCCCGGATTGATCTACCGAATGAAGCAGCCTAAGATCGTGCTCCTGATCTTCGTCTCTGGAAAGATTGTGCTTACTGGTGCAA

upper sequence: PP1S246_34V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 6
agaatttaaaatgttacaaaatgagctgctttaagtgcctaaactatctttcagatcttattggtgtttgacccatgaactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
                 ||   | ||| | ||     |    |   |||||    |||| |  | || | | |  | || | |||          ||||||| ||||||||| ||||||| || ||||| ||  ||||||||||||| ||||| ||  | || |||||||| |||||||||||||| ||||||||||| |
---------------gtaagtcgtgcttcctttgtcacacttatactcttttc--tcttttgcgggtcttatcactaaagttttg----------tgcagTACGAACCAGAGCTGTTCCCCGGATTGATCTACCGAATGAAGCAGCCTAAGATCGTGCTCCTGATCTTCGTCTCTGGAAAGATTGTGCTTACTGGTGCAA

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|208373747|gb|DC936560.1|DC936560
EST:     TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAGGT                         TATGAACCAGAGTTGTCCCCAGGGTTGATATATAGAATGAAGCAGCC-AAG
genomic: TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
EST: gi|162267516|gb|FC444267.1|FC444267
EST:     TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT                         TATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
genomic: TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
EST: gi|208373112|gb|DC948877.1|DC948877
EST:     GAGGGTTTAGCATATGCCCATGGTCA-TTTTCAAGT                         TATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
genomic: GAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
EST: gi|37844368|gb|BJ602376.1|BJ602376
EST:     GGGTTTAGCATATGCCCCATGGTCATTTTTCAAGT                         TATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
genomic: GGGTTTAGCATATG-CCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
EST: gi|162267515|gb|FC444266.1|FC444266
EST:     TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT                         TATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
genomic: TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
EST: gi|208360850|gb|DC934746.1|DC934746
EST:     TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCA-GT                         TATGAACCAGAGTTGTTCCNAGGGTTGATATATAGAA
genomic: TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAA
EST: gi|208382418|gb|DC927952.1|DC927952
EST:     TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT                         TATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
genomic: TCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
EST: gi|208396134|gb|DC924600.1|DC924600
EST:     CTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGT                         TATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
genomic: CTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAG
EST: gi|100410692|gb|BY992221.1|BY992221
EST:     CCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTTCA-GT                         TATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAA
genomic: CCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTT-CAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAA

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

GACTTCAAAATTCAGAATATTGTTGGATCATGTGACGTGAAGTTCCCTATCCGGCTCGAGGGTTTAGCATATGCCCATGGTCATTTTTCAAGTgtgagcactc ... ctgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttcagatcttattggtgtttgacccatgaactgttggttcactgtttgcagTATGAACCAGAGTTGTTCCCAGGGTTGATATATAGAATGAAGCAGCCCAAGATTGTATTGCTTATCTTCGTGTCTGGAAAGATTGTCCTTACTGGTGCTA
                    gtttgac  putative branch site (score: 2)
         atcttatt  TA-rich tract