Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtatcctatgcactttcttgttctatgagtaacttggctgtaatcatggcgtacgtgtgatacagtgcgtgagacgttcgttatttgcgttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG

Basic information

species Physcomitrella patens
transcript PP1S37_166V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA18G46940.1 (Glycine max), 3'ss of exon 3
------------------------agtatcctatgcactttcttgttctatgagtaacttggctgtaatcatggcgtacgtgt-gatacagtgcgtgagacgttcgttatttgcgttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG-
                        |  ||  | || | |   | ||| ||   ||   || | | |||  ||    |  |||| | | |      |  ||   || |   |  | ||  || |||||||||||| || ||  ||||||| |||||||| || |||||||||||||| | 
taagcacatagtagtaatgctctgaaaattgtctgtattgagtagtt-tacatgtgtattagatataagaataat-tgtgtgtcggtgcgtctgatctgatcatcttggataacattaatttcaggTCAGGATCAGTTTGTCTGGATGTTATCAATCAAACCTGGAGTCCCATGTTTGG

upper sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G01980.1 (Glycine max), 3'ss of exon 4
agtatcctatgcactttcttgttctatgagtaacttggctgtaatca-----tggcgtacgtgtgatacagtgcgtgagacgttcgttat-ttgcgttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG
      ||  | | | ||  ||   |  |  ||||||    | ||       | | |      ||    | | |       | ||  ||  || | |    ||||| || || |||||||||||||||||||| || ||  |||||||||| |||||||
------cttagaagtatcaagtcacagaaacaacttgctattgattggtgttttgtgcgtacatggattattactcattctgctctgtacgtttcatcacctgcagATCTGGCTCTGTATGCTTGGATGTCATTAACCAATCTTGGAGTCCAATGTTCG

upper sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 3
-------------------------------------------agtatcctat-------gcactttcttgttctatgagtaacttggctgtaatcatggcgtacgtgtgatacagtgcg-tgagacgtt--cgttatttgcgttggt-tgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG
                                             |||| |||       ||||  |  || || ||| | |   |    |   |     |  ||   |   | |   |  |    | ||    | |||| |  || | |  ||||| || ||||| ||||| ||||| || || |||||||||||||||||||| |
gtaagttgtttcactgcaaccatagcttcattgaatcattgtttatatcatatttaagcagcacaattatgctccatgggaagtctattggctgttgca-caaacacattgcaaaactcacttgctcattaatatgattttctctgatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTG

upper sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv17s0000g07960.t01 (Vitis vinifera), 3'ss of exon 5
agtatcctatgc-actttcttgtt-ctatgagtaacttggctgtaatcatggcgtacgtgtgatacagtgcgtgagacgttcgttatttgcgttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG
  | ||  ||   ||    ||||| | ||   ||| ||   | |     | |    |  ||   |   |      |  |    || |||   |    ||||||||||| |||||||||||||||||||| || ||  | |||||||| ||||| |
gctgtcagatttgacgactttgtttccatttttaattttttttttgaagtagttggcaagtccca-gctaaactggttgcatatttttt-tatgaactgcagGTCAGGTTCTGTATGCTTGGATGTCATTAACCAATCATGGAGTCCAATGTTTG

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|67573456|gb|BJ946280.1|BJ946280
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTANATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCA
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCA
EST: gi|208369538|gb|DC936314.1|DC936314
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAAATGAAAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCANACTTGGANTCCCATGT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGT
EST: gi|100387725|gb|BY951725.1|BY951725
EST:     CCTTNCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGA
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGA
EST: gi|100387203|gb|BY970347.1|BY970347
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|22492750|gb|BU052673.1|BU052673
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|67696838|gb|BJ957071.1|BJ957071
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|208400064|gb|DC908627.1|DC908627
EST:     CCTTCCATTGGGTTTGTGAATANGATCTTCCATCCCAACGTAAATGAAAT                         GTCAGGATCTGTATGCTTGGANGTCATCAATCAAACTNGGANTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162201846|gb|FC377780.1|FC377780
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|67696647|gb|BJ956880.1|BJ956880
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162268532|gb|FC444405.1|FC444405
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162261485|gb|FC438321.1|FC438321
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|67573262|gb|BJ946086.1|BJ946086
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAG
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAG
EST: gi|162260434|gb|FC436087.1|FC436087
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162274058|gb|FC450130.1|FC450130
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|208353497|gb|DC922509.1|DC922509
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|208348460|gb|DC901951.1|DC901951
EST:     CCTTCCATTGGGTTTGTGAATANGATCTTCCATCCCAACGTANATGANAT                         GTCANGATCTGTATGCTTGGATGTCATCAATCANACTTGNANTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|208374764|gb|DC948694.1|DC948694
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|208396037|gb|DC915797.1|DC915797
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|208358398|gb|DC934563.1|DC934563
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAAATGANAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAAACTTGGA
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGA
EST: gi|37851038|gb|BJ609046.1|BJ609046
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162201845|gb|FC377779.1|FC377779
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|208399979|gb|DC905005.1|DC905005
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAAATGANAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162274057|gb|FC450129.1|FC450129
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162222561|gb|FC398712.1|FC398712
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|100377520|gb|BY986284.1|BY986284
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCA
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCA
EST: gi|208361846|gb|DC950118.1|DC950118
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|37832758|gb|BJ590770.1|BJ590770
EST:     CATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|208378275|gb|DC918896.1|DC918896
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|37851815|gb|BJ609823.1|BJ609823
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162261484|gb|FC438320.1|FC438320
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
EST: gi|162268531|gb|FC444404.1|FC444404
EST:     CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGAT                         GTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT
genomic: CCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTT

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: 32 (upstream exon), 21 (downstream exon)
Score: 5

GAACCTGGAAGATCCGAGTCGAATTGCCTGATGCTTATCCCTACAAGTCTCCTTCCATTGGGTTTGTGAATAGGATCTTCCATCCCAACGTAGATGAGATgtaagatatt ... ttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggcgtacgtgtgatacagtgcgtgagacgttcgttatttgcgttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG
                                    ttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtatcctatgcactttcttgttctatgagtaacttggctgtaatcatggcgtacgtgtgatacagtgcgtgagacgttcgttatttgcgttggttgcagGTCAGGATCTGTATGCTTGGATGTCATCAATCAGACTTGGAGTCCCATGTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG