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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgtgtagcgagtgctcatagttgtatgcacttttttgtaattgtttcggtcaatatggggattgttgcggtgtctgaacttgaattgtgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAGACTATCTTCGTGTTCGGCTTCAGGACCCAATTTGGAGGTGGCAAGTCCA

Basic information

species Physcomitrella patens
transcript PP1S37_112V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_112V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g52490.1 (Oryza sativa), 3'ss of exon 2
gtgagtttgtgtagcgagtgctcatagttgtatgcacttttttgtaattgtttcggtcaatatggggattgttgcggtgtctg-aacttgaattgtgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAGACTATCTTCGTGTTCGGCTTCAGGACCCAATTTGGAGGTGGCAAGTCCA
             | |||  |||   | ||||    |||   |||  | ||   | |  || || ||   |||  | | || |   || |  || ||  || ||||| ||||||||||||||||| |||||||| ||||| ||    ||| |  |    ||||||||||||   ||| | ||||| || || || ||||||||||
-------------gtgagacctc---ggtgtaaat-cttacatgtggtggtggtgat-gatttgcggggggtttggatctcagcggctggggttttgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA
















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|18368342|gb|BJ200427.1|BJ200427
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|37849875|gb|BJ607883.1|BJ607883
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67709358|gb|BJ965174.1|BJ965174
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67718399|gb|BJ968658.1|BJ968658
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|18344985|gb|BJ177026.1|BJ177026
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67723513|gb|BJ973772.1|BJ973772
EST:     ACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|162249820|gb|FC427597.1|FC427597
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67709437|gb|BJ965253.1|BJ965253
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67722459|gb|BJ972718.1|BJ972718
EST:     TGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: TGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67703265|gb|BJ963498.1|BJ963498
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67723434|gb|BJ973693.1|BJ973693
EST:     CCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: CCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67727511|gb|BJ977770.1|BJ977770
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67703950|gb|BJ964183.1|BJ964183
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67691760|gb|BJ951993.1|BJ951993
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|162211671|gb|FC387959.1|FC387959
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|162249821|gb|FC427598.1|FC427598
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67728039|gb|BJ978298.1|BJ978298
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|162202366|gb|FC379179.1|FC379179
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|162269513|gb|FC445069.1|FC445069
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|208345424|gb|DC912999.1|DC912999
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67719775|gb|BJ970034.1|BJ970034
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|162269512|gb|FC445068.1|FC445068
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67719209|gb|BJ969468.1|BJ969468
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|18346009|gb|BJ178052.1|BJ178052
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|37825126|gb|BJ583192.1|BJ583192
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67724705|gb|BJ974964.1|BJ974964
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGACGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|18361756|gb|BJ193823.1|BJ193823
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67716187|gb|BJ966447.1|BJ966447
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGACGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|37824188|gb|BJ582254.1|BJ582254
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|67574155|gb|BJ946979.1|BJ946979
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
EST: gi|208355156|gb|DC926765.1|DC926765
EST:     ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAG                         GCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG
genomic: ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAG

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: 34 (upstream exon), 31 (downstream exon)
Score: 81

ATCATTGATGTTCTTCACCCTGGTCGTGCCAATGTCTCGAAGgtgagtttgt ... tgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAGACTATCTTCGTGTTCGGCTTCAGGACCCAATTTGGAGGTGGCAAGTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcggtcaatatggggattgttgcggtgtctgaacttgaattgtgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAGACTATCTTCGTGTTCGGCTTCAGGACCCAATTTGGAGGTGGCAAGTCCA
       tcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttgtgtagcgagtgctcatagttgtatgcacttttttgtaattgtttcggtcaatatggggattgttgcggtgtctgaacttgaattgtgtggttcagGCCGAGCTGAAGGAGAAGCTTGCCAAGCTTTACGAAGTTCGTGACCCTCAGACTATCTTCGTGTTCGGCTTCAGGACCCAATTTGGAGGTGGCAAGTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG