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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT

Basic information

species Physcomitrella patens
transcript PP1S60_129V6.1
intron # 2
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 2
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 3'ss of exon 1
---ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
    |||||       | || | | ||   |   |  |||    |    |       |   ||| ||   ||||||    |   ||    || |   ||  |||||| || |||||| | || || || ||||||||| | |||||||| || || || ||||| |||||||||||||| |||||||| |  || ||  ||| 
attcttttttgggatttcaagcctcatgagtagctgcatacagaacaaatctagtaattcatttattgaattctttactgtgctgag---tacatctctgcagTTCCCAGAAACTTTAGACTGCTTGAAGAGCTTGAGCGAGGTGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATA

upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G35790.1 (Glycine max), 3'ss of exon 1
--ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
  |||  |  || | | | |  |        | || |||| | ||      |||  | ||    |   | | |  | || | | |  | ||    | |  |||||| ||||||||  |  | || ||||||||||||| ||| || ||||| ||||| ||||| ||||| |||||||| |||||||| || |||||  | | 
aatttggttgaaggattacatatgtagccattcttgatattt-attgaagatacaatgttagcatgagtatgtagttaa-aggcatttgtactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATCGGAGATGGAACAGTTAGCTATGGAATGGATGATGGTGACGACATTTA

upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA02G35990.1 (Glycine max), 3'ss of exon 1
--------ttttttcaaatgctgaaact-taatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
        | || |||     |||  |   |||   |  ||  || | |     | |  |        | ||| | |||| ||||||||     | | |  || |  |||||||||||||||  |  | || |||||||||||  | ||||| ||||| || || ||||||||||| |||||||| |||||||| || || ||  | | 
gtagatattcttgtcatgaattgatcccacaatggctagttacatgttttcaaataaaaaa-------tgtttgtgttctgttaaatatttg--tatgtttaaatgcagTTCCTAGGAACTTCAGATTGCTGGAGGAGCTTGAACGTGGTGAAAAAGGAATTGGAGATGGCACAGTTAGCTATGGAATGGATGATGGTGATGACATTTA

upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 1
ttttttcaaatgctg-aaacttaatttttgtttttatatctgatccttagt--accttcttttttttcttttcttttaaatatgg-aactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
       | ||| || ||   | || | |||    ||   ||||  ||| |  |  | |  | |     |   | |  | || || || |  |    | |  |||||| ||||||||  |  | || ||||||||||||| ||| || ||||| || || ||||||||||| || ||||| |||||||| || || ||  | | 
----aaaatatggtggaaggattatatatgtagccattcttgatatttattgaagatacaatgtcagtatgagtgtgtagtaaggcaattgcactttaatgcagTTCCAAGGAACTTCAGATTGCTGGAGGAGCTTGAGAAGGGAGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTA

upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 1
ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaa----ctatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
|   ||||   |    |    || | ||    ||| |       ||| | |   | |  |    |||   ||| |||| |     | |  |       ||  |||||||||||| ||  |  |  |  | ||||||||||| |||||||| || || || ||||| || || |||||||| ||||||||||  |||||  ||| 
tgccttcatcagtcatattgcaactatttcaattaaacag----ctttgaaggatttaatagaacttagatttgaaatttactcttcttaattggtccctgcagTTCCTAGGAATTTCAGATTATTGCAAGAGCTTGAGAGAGGTGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATA

upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 3'ss of exon 1
---ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttctttttt---ttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
   | |  ||  || |     ||  |||      | |||||||||||  ||  |   | |  |||     |  |  || |||       | ||| |     | ||||||| ||||||||| |  |  | || |||||||| || |||||||||||||| || ||||| || || |||||||| |||||||| |  || ||| | | 
gaatgtgatcggatccatggtctcgatt---aggtatatatctgatctgtaaaatgatttgatttgggggcgatatttataagagcttgattttgtga---tgtagTTCCGAGGAACTTTAGATTGTTGGAAGAGCTTGAAAGAGGTGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTA

upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G36060.3 (Arabidopsis thaliana), 3'ss of exon 1
-----ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
     | |||||||   | |    ||    || |  | || | || ||   |  ||  ||| ||     ||     || |  | |   |  || |  |  || |||||| ||||| || ||  | || |||||||||||  | || ||||||||||| || ||||| || ||||||||||| |||||||| || || ||  | | 
tagattgttttcaagctcagtgctttg--cttagaatatagagcttatttgtgttagtttccttca---ctaaaaattgagctgtttgatgttgttaatgtaaagTTCCGAGGAATTTCCGGTTGCTGGAGGAGCTTGAACGTGGAGAGAAAGGTATTGGAGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATTTA

upper sequence: PP1S60_129V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G52560.4 (Arabidopsis thaliana), 3'ss of exon 1
ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttctt--------ttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
       | ||| |      |  | | || ||| ||     |   | | | | |  |||  |||  |        || ||||   || |    ||  | ||| ||||||||| ||||| |||||  |  | |||||||||||  | || ||||||||||| || ||||| || ||||||||||| |||||||| || || ||  | | 
-------atatgatatgttctgttctctgctttgattaaaaaaagtgattgcttgttttcatttactgatatgaattgtttttgttacgcttgttattgcaa-tatagTTCCGAGGAATTTTCGGTTGTTGGAGGAGCTTGAACGTGGGGAGAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTA

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:     AAGATTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|7584254|gb|AW700150.1|AW700150
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|22132526|gb|BQ827212.1|BQ827212
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|22132462|gb|BQ827175.1|BQ827175
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|162240765|gb|FC417475.1|FC417475
EST:     GCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: GCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|67574644|gb|BJ947468.1|BJ947468
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|15729419|gb|BI741306.1|BI741306
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|162224222|gb|FC399494.1|FC399494
EST:     AAGATTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|67571600|gb|BJ944424.1|BJ944424
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|67694950|gb|BJ955183.1|BJ955183
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|162227636|gb|FC402629.1|FC402629
EST:     AAGATTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|67698060|gb|BJ958293.1|BJ958293
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|18371364|gb|BJ202966.1|BJ202966
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
EST: gi|18346800|gb|BJ178845.1|BJ178845
EST:     AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTG                         TTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA
genomic: AAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTA

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: 33 (upstream exon), 34 (downstream exon)
Score: 19

AATTTAGAGACTTTTCGTGCTCAAGAGTGCGGAAGTAGCCATCTGAGATGATTACAGGGGGCTCTGTAGTTGgtaagcttct ... acaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtaccttcttttttttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT
           ttttttttcttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttttcaaatgctgaaacttaatttttgtttttatatctgatccttagtaccttcttttttttcttttcttttaaatatggaactttatacaactatagTTCCTAGGAACTTTCGTCTTCTCGAGGAGCTTGAGAGGGGTGAGAAAGGTATCGGCGATGGCACAGTGAGCTATGGCATGGATGACGGCGACGATGTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - tgctgaa