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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaattagggtttccggttttacatactggtgtttagggtgttgatactagtattagttctggcgatagtgatcgtttccttggcacgtccttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA

Basic information

species Physcomitrella patens
transcript PP1S47_40V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_40V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDO97033 (Chlamydomonas reinhardtii), 3'ss of exon 1
ttaattagggtttccggttttacatactggt-gtttagggtgttgatactagta----ttagttctggcgatagtgatcgtttccttggcacgtccttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA
  |   || | | | |     ||   | | | |    | |||   ||||  | |      | |    ||||   ||||  ||  |||||   || |    || |||||||||||| || |||||||||||  | || |  |||||||||||||| || |||||||||||| | ||||| |||||||| || ||||||||||| ||
--agccagagct-cagaggcgacgcccagctcgacatgagtgggaatacgtgcaacttcaaatggaagcgacgctgatttttggcttgggctgtgcac--tgcagATGGCAAGACCTTCAAGAAGCCCCGGCGTCCTTATGAGAAGGAGCGCCTGGACGCTGAGCTGAAGCTTGTCGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S47_40V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ11758 (Selaginella moellendorffii), 3'ss of exon 1
ttaattagggtttccggttttacatactggtgtttagggtgttgatactagtattagttctggcgatagtgatcgtttccttggcacgtccttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA
                                  || |    |  | || |      ||  | |  |   ||||| | |   ||   | |      | |||||| || ||||| |||||||| ||  |||| ||||||||||||||||| || || ||||| ||| |||| || |||||||| || ||||||||||| ||
---------------------------------gtaagtctctccttctcgatcgcattgcgcccgtgccgatcgatcc---ggtgtgcc------gcagATGGGAAAACTTTCAAGAAGCCACGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S47_40V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ31761 (Selaginella moellendorffii), 3'ss of exon 1
ttaattagggtttccggttttacatactggtgtttagggtgttgatactagtattagttctggcgatagtgatcgtttccttggcacgtccttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA
                                          | |  || | ||| |  |||||  | |     |  || | |    |    |   | |||||| || ||||| |||||||| ||  |||| ||||||||||||||||| || || ||||| ||| |||| || |||||||| ||||| |||||||| ||
-----------------------------------------gtaagtctcg-attcgcgctggcagtcgccg--ggatcatggatttggtggtgtcgcagATGGGAAAACTTTCAAGAAGCCGCGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGGCTCCGGAACAAGCGAGA

upper sequence: PP1S47_40V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ13465 (Selaginella moellendorffii), 3'ss of exon 1
ttaattagggtttccggttttacatactggtgtttagggtgttgatactagtattagttctggcgatagtgatcgtttccttggcacgtccttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA
                                  || |    |  | || |      ||  | |  |   ||||  | |   ||   | |      | |||||| || ||||| |||||||| ||  |||| ||||||||||||||||| || || ||||| ||| |||| || |||||||| || ||||||||||| ||
---------------------------------gtaagtctctccttctcgatcgcattgcgcccgtgccgatccatcc---ggtgtgcc------gcagATGGGAAAACTTTCAAGAAGCCACGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S47_40V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ38391 (Selaginella moellendorffii), 3'ss of exon 1
ttaattagggtttccggttttacatactggtgtttagggtgttgatactagtattagttctggcgatagtgatcgtttccttggcacgtccttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA
                                          | |  || | ||| |  || ||  | |     |  || | |    |    |   | |||||| || ||||| |||||||| ||  |||| ||||| ||||||||||| || || ||||| ||| |||| || |||||||| ||||| |||||||| ||
-----------------------------------------gtaagtctcg-attcgcgcttgcagtcgccg--ggatcatggatttggtggtgtcgcagATGGGAAAACTTTCAAGAAGCCGCGGCGGCCATTCGAAAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGGCTCCGGAACAAGCGAGA

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|18345488|gb|BJ177531.1|BJ177531
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|18343350|gb|BJ175388.1|BJ175388
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|18373410|gb|BJ204988.1|BJ204988
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|162258349|gb|FC434276.1|FC434276
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|208351530|gb|DC905707.1|DC905707
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|162225472|gb|FC401224.1|FC401224
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|162264179|gb|FC440241.1|FC440241
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|162250877|gb|FC426921.1|FC426921
EST:     CTCTGTT-GCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|18355636|gb|BJ187695.1|BJ187695
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|162279610|gb|FC455869.1|FC455869
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|18343142|gb|BJ175180.1|BJ175180
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|19782393|gb|BQ039848.1|BQ039848
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|162268456|gb|FC444329.1|FC444329
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|18369370|gb|BJ201456.1|BJ201456
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|19790182|gb|BQ041741.1|BQ041741
EST:     GCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: GCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|162249996|gb|FC427097.1|FC427097
EST:     TTCGTTCGGCAATT                         ATGGCAAGACTTTTAAGAAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTT
genomic: TTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAG-AAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTT
EST: gi|18362283|gb|BJ194353.1|BJ194353
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|162250878|gb|FC426922.1|FC426922
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|18326314|gb|BJ158313.1|BJ158313
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
EST: gi|67508165|gb|BJ941036.1|BJ941036
EST:     CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATT                         ATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG
genomic: CTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTG

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: 26

TCTCTTTCCACGCTTGCGATTGTAGTTGGTTGGAAGCTCTGTTGGCTTCAACGCAAAAATGGTGCACGTCGCTTCGTTCCGCAATTgtaagtcatc ... cttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactagtattagttctggcgatagtgatcgtttccttggcacgtccttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA
                                         cgtccttc  CT-rich tract
      tattagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaattagggtttccggttttacatactggtgtttagggtgttgatactagtattagttctggcgatagtgatcgtttccttggcacgtccttcgtgtagATGGCAAGACTTTTAAGAAGCCCCGCAGGCCCTTCGAGAAGGAGCGCCTTGATGCTGAGCTGAAGTTGGTCGGAGAGTATGGTCTCCGCAACAAGCGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG