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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttcatgatgtgtatgtttctgcgcagcttaagttgcctccatcccaatgttttgtaactgagttgtcatcgacacattcaaactgctttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGACTATCCCGACAAGCCTCCAACTGTTAGATTCCACTCCCGAATCAATATGA

Basic information

species Physcomitrella patens
transcript PP1S60_129V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G071010_T01 (Zea mays), 3'ss of exon 2
-tggttcatgatgtgtatgtttctgcgcagcttaagttgcctccatcccaatgttttgtaactgagttgtcatcgacacattcaa-actgctttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGACTATCCCGACAAGCCTCCAACTGTTAGATTCCACTCCCGAATCAATATGA
   ||   |  | | ||     | |||||   |            | |   | ||   || || | || |   |    |   ||| | | || ||||| ||| |||| || || ||||| ||||||    ||||||| ||||| |||||||||||||| || ||||| ||| |||| |||||||||||  ||||||| ||||
tctgtaggtcttctcta-acaacagcgcattcttttccatagagttgcttctcttggctatctaatttatttccacgtcccacaacatttctctttgt-cagACTGTACATGAGGGTCGCATCTACCAGCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGA

upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G027378_T01 (Zea mays), 3'ss of exon 2
-tggttcatgatgtgtatgtttctgcgcagcttaagttgcctccatcccaatgttttgtaactgagttgtcatcg-acacattcaaactgctttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGACTATCCCGACAAGCCTCCAACTGTTAGATTCCACTCCCGAATCAATATGA
   ||   |  | | ||     | ||||||  |            | |   | ||   || || | ||||   |     ||   | | | || ||||| ||| |||| || || ||||| ||||||    ||||||| ||||| ||||| |||||||| || ||||| ||| |||| |||||||||||  ||||||| ||||
tctgtaggtcttctcta-acaacagcgcagtcttttccatagagttacttctcttggctatctaatttgtttccacgtccaacaacatttctctttgt-cagACTGTACATGAGGGTCGCATCTACCAGCTGAAGTTGTTTTGTGACAAAGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGA
















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|162211928|gb|FC387800.1|FC387800
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|7584254|gb|AW700150.1|AW700150
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|22132526|gb|BQ827212.1|BQ827212
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|22132462|gb|BQ827175.1|BQ827175
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|162240765|gb|FC417475.1|FC417475
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|67574644|gb|BJ947468.1|BJ947468
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|15729419|gb|BI741306.1|BI741306
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|162224222|gb|FC399494.1|FC399494
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|67571600|gb|BJ944424.1|BJ944424
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|67694950|gb|BJ955183.1|BJ955183
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|22492518|gb|BU052441.1|BU052441
EST:     GGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTA-TTTGCGACAAGGAC
genomic: GGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|7584264|gb|AW700160.1|AW700160
EST:     ATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|162227636|gb|FC402629.1|FC402629
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|67698060|gb|BJ958293.1|BJ958293
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|18371364|gb|BJ202966.1|BJ202966
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|162227635|gb|FC402628.1|FC402628
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|22492562|gb|BU052478.1|BU052478
EST:     ACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|18329558|gb|BJ161564.1|BJ161564
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|18346800|gb|BJ178845.1|BJ178845
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
EST: gi|37851532|gb|BJ609540.1|BJ609540
EST:     ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCAT                         TCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC
genomic: ACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGAC

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), 35 (downstream exon)
Score: 40

TGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATTTATGCGCTCTTGGACCGGCACTATCATTGGACCAAGCCATgtgagttcct ... ttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGACTATCCCGACAAGCCTCCAACTGTTAGATTCCACTCCCGAATCAATATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccaatgttttgtaactgagttgtcatcgacacattcaaactgctttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGACTATCCCGACAAGCCTCCAACTGTTAGATTCCACTCCCGAATCAATATGA
         ttgtaac  putative branch site (score: 40)
                                        ctgcttttt  putative PPT
       ttttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggttcatgatgtgtatgtttctgcgcagcttaagttgcctccatcccaatgttttgtaactgagttgtcatcgacacattcaaactgctttttgtgcagTCTGTCCACGAAGGTCGGATCTACACATTGAAGTTATTTTGCGACAAGGACTATCCCGACAAGCCTCCAACTGTTAGATTCCACTCCCGAATCAATATGA

- - - - - - - - - - -ctgcgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacattc