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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccagtgtcatctcgtcataatgaccgcacgtttaattctgaagtcgcctccccagtcttcgttaccatgtgcaactaacaccactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG

Basic information

species Physcomitrella patens
transcript PP1S54_156V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 3
atccagtgtcatctcgtcataatgaccgcacgtttaattctgaagtcgcctccc-cagtcttcgttaccatgtgcaactaac--accactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
                      | |     | |   |||||      || |    ||   |  ||     ||| ||   | |    ||  | || | || ||||||| ||||||||||| ||||| |||||| | || || || ||||||||  | ||||| ||||||||||||||||| || |||||||| || |||
---------------------gtaattaagcatcctattctttgcctgcataatgcaacatgagtatttctgttcattcatccagacatcgataattgtacagAGATCATGGATTTTGGTTATCCTCAAAACCTGTCACCTGAAATTTTGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA17G16630.3 (Glycine max), 3'ss of exon 3
atccagtgtcatctcgtcataatgaccgcacgtttaattctgaagtcgcctccccagtcttcgttacc-------atgtgcaactaacaccactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
    |   | || | ||  | | | ||  |   | |||||||     |       | |  | || |          ||    | ||  |||  | || ||  |||||| |||||||| ||||| || || |||||  | || |||||||| || || |||||||| ||||| ||||| || ||||| |||||||||||||||
----acgtttatttagtgttgaaggccagag--taaattctgtgagagagaaaaaaatacttgtcatttaaatgggtgaatgattattacctattttgttt-tgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 3
atccagtgtcatctcgtcataatgacc---gcacgtttaattctgaagtcgcctccccagtc-ttcgttaccatgtgcaactaacacc-actgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
    |   | || |  |  | | | ||   | |  ||   |  |  ||        |  ||| ||        ||    | ||  ||| | |||| ||  |||||| |||||||| ||||| || || |||||  | || |||||||| || || |||||||| ||||| ||||| || ||||| ||||||||||| |||
---aaaatttatttaatgttgaaggccagtgtaaattctgtgatagagaaaaaatacttgtcatttaaatgggtgaatgattattacctattgttttt--tgcagAAATTATGGACTTTGGTTACCCACAAAATCTTTCACCAGAGATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCAAAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA01G40700.1 (Glycine max), 3'ss of exon 3
atccagtgtcatctcgtcataatgaccgcacgtttaattctgaagtcgcctccccagtcttcgttaccatgtgcaactaac-accactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
 || |   |    |  | ||||    | ||  |    |||| | |          | |  || ||   || || |  |    |  |    |||   | |||| || ||||| ||||| ||||| |||||  | || || || || || || |||||||| ||||| ||||| || ||||| |||||||||||||||
ttcaaactttgcataataataaaagaccca-atagtgttctcatgatagaaaaatatttatcatttgaatttgaatgtgtttatgataaatatatttacagAAATCATGGACTTTGGTTATCCTCAAAATCTTTCACCGGAAATCTTAAAGCTTTATATCACTCAGGAAGGAGTGCGTTCCCCATTTTCATCCAAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G46630.2 (Arabidopsis thaliana), 3'ss of exon 3
---atccagtgtcatctcgtcataatgaccgcacgttt-----aattctgaagtcgcctccccagtc-ttcgtta--ccatgtgcaactaacaccact----gttattcg---------tgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
   |   ||  | ||   ||||| || |   ||| ||      | || | |||| || |     ||  |  ||||  | || |     |||||||| |    | ||||           ||||||||||||||| ||||| ||||| |||||  | || || || ||||| ||||||||||| ||||| |||||||| || || ||||||||||| |||
gtaagtaagcctgatagggtcatgatcaaatcactttcttatcacttgtaaagttgcattagtcgttatatgttattctattttgtggtaacaccaatgaatgatattttgtattgaattgcagAGATTATGGACTTTGGCTATCCACAAAATCTCTCACCTGAAATTTTAAAACTTTATATCACTCAGGAAGGTGTACGGTCACCATTTTCATCGAAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 3
atccagtgtcatctcgtcataatgaccgcacgtttaattctgaagtcgcctccccagtcttcgttaccatgtgcaactaacaccactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
                                               |  |   |    || | |  ||||   || | |   | || ||    |||||||||| ||||| ||||| || || |||||  | || || ||||||||||| || ||||| ||||| || ||||||||||| ||||| ||    |||
-----------------------------------------------gtattttcg---tttggtttcatggaaaattcatcacgcttttgaatgtgcagAGATCATGGACTTTGGATACCCGCAAAATCTTTCTCCTGAGATTTTGAAGCTCTATATAACTCAGGAGGGTGTTCGTTCGCCATTCTCG---AAG

upper sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 3
atccagtgtcatctcgtcataatgaccgcacgtttaattctgaagtcgcctccccagtcttcgttaccatgtgcaactaacaccactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
                                               |  |   |    || ||| |   |   |   | |||   | | |   |||||||||| ||||| ||||| || || |||||  | || || ||||||||||| || ||||| ||||| || ||||||||||| ||||| ||    |||
-----------------------------------------------gtattttcg--tttggtttctcggaaaattcatcacacttttgaaatgtgcagAGATCATGGACTTTGGATACCCGCAAAATCTTTCTCCTGAGATTTTGAAGCTCTATATAACTCAGGAGGGTGTTCGTTCGCCATTCTCG---AAG

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|18331306|gb|BJ163315.1|BJ163315
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCC
EST: gi|100401870|gb|BY954751.1|BY954751
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|162280315|gb|FC456332.1|FC456332
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|18342109|gb|BJ174144.1|BJ174144
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGT
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGT
EST: gi|100404582|gb|BY973650.1|BY973650
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|18343908|gb|BJ175946.1|BJ175946
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACNAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|100407280|gb|BY974093.1|BY974093
EST:     TGAGGATGCGATCAGCAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|208385555|gb|DC937100.1|DC937100
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|100429936|gb|BY978164.1|BY978164
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|67572605|gb|BJ945429.1|BJ945429
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|208361334|gb|DC935063.1|DC935063
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|100384770|gb|BY950760.1|BY950760
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|162223092|gb|FC399983.1|FC399983
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|100407158|gb|BY974039.1|BY974039
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGGAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|18327379|gb|BJ159381.1|BJ159381
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGG
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGG
EST: gi|100387570|gb|BY988441.1|BY988441
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|67578518|gb|BJ950685.1|BJ950685
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|18328150|gb|BJ160154.1|BJ160154
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|208393441|gb|DC904059.1|DC904059
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|100415400|gb|BY975297.1|BY975297
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGANTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|100450131|gb|CJ974109.1|CJ974109
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTCTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|100450358|gb|CJ974223.1|CJ974223
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
EST: gi|100364351|gb|BY984569.1|BY984569
EST:     TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATG                         AGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC
genomic: TGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAAC

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: 31 (upstream exon), 35 (downstream exon)
Score: 13

GCAGTCGCACTTTTCAAGTCGTACTTTGGAGGGGCGTTCGATGAGGATGCGATCAGGAATAATTTTGTGCTCATCTACGAGCTTCTTGATGgtgtggaacc ... attcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcctccccagtcttcgttaccatgtgcaactaacaccactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG
                             aactaac  putative branch site (score: 13)
                                         tgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccagtgtcatctcgtcataatgaccgcacgtttaattctgaagtcgcctccccagtcttcgttaccatgtgcaactaacaccactgttattcgtgcagAGATTATGGATTTTGGGTATCCCCAAAACTTATCCCCAGAGATTTTGAAACTTTATATTACTCAAGAAGGTGTTCGTTCTCCATTTTCATCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG