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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttgcatgctttcttaatgctttcattttcttcttacgttagcggttgattcactcagacctctaaaactggttctatgtaattcttgtggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTGCTATTGGGAGCCGACAACGCCGCCATTAAAGAGAACCGG

Basic information

species Physcomitrella patens
transcript PP1S540_7V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 5
tatttgcatgctttcttaatgctttcattttcttcttacgttagcggttgattcactcagacctctaaaactggttctatgtaattcttgtggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTGCTATTGGGAGCCGACAACGCCGCCATTAAAGAGAACCGG
                |||     |   ||||   ||  |  |||| ||   |||     |  ||   || |  | |     | |   ||     ||||||| ||||| ||||||||  | || || ||||||||||||||||| ||||||||||| ||||| |   |  | |  ||||| ||  |  | 
---------------gtaacttggtttatttcaaattgtgcaagcgattacatcatcagaatatcactaaattatacctcaca-tggatggaacttgcagTATCTTCCAATTGAGGGGTTGGCAGCATTCAACAAGGCTACTGCTGAGTTGCTATTTGGAGCTGGTCATCCTGTTATTAAGGAACAAAGA

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ05582 (Selaginella moellendorffii), 3'ss of exon 2
tatttgcatgctttcttaatgctttcattttcttcttacgttagcggttgattcactcagacctctaaaactggttctatgtaattcttgtggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTGCTATTGGGAGCCGACAACGCCGCCATTAAAGAGAACCGG
                                       || |||  |||| |   | |    | |     |  ||   | |  || ||||    | ||||| ||||| ||||| || ||||||||||| |||||||||||||| ||| | || ||||| || |||||  | |  || ||  |   || |
---------------------------------------gtgagc--ttgaatgtttgaaggttttggtgttcattggttttcgtttttgtatcatacagTATCTTCCAATTGAAGGTCTTGCTGCTTTTAACAAGGCTACTGCCGAGCTTCTGTTGGGGGCTGACAATCCAGTAATCAAGAATGGCCAG

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ26197 (Selaginella moellendorffii), 3'ss of exon 2
tatttgcatgctttcttaatgctttcattttcttcttacgttagcggttgattcactcagacctctaaaactggttctatgtaattcttgtggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTGCTATTGGGAGCCGACAACGCCGCCATTAAAGAGAACCGG
                                       || |||  |||| |   | |    | |     |  ||   | |  || |||     | ||||| ||||| ||||| || ||||||||||| |||||||||||||| ||| | || ||||| || |||||  | |  || ||  |   || |
---------------------------------------gtgagc--ttgaatgtttgaaggttttggtgttcattggttttcgtttttg-atcatacagTATCTTCCAATTGAAGGTCTTGCTGCTTTTAACAAGGCTACTGCCGAGCTTCTGTTGGGGGCTGACAATCCAGTAATCAAGAATGGCCAG

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|208372110|gb|DC940292.1|DC940292
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|67574849|gb|BJ947673.1|BJ947673
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|18374954|gb|BJ206532.1|BJ206532
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|100359406|gb|BY984238.1|BY984238
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|67570023|gb|BJ942847.1|BJ942847
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|100369975|gb|BY967466.1|BY967466
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|18366753|gb|BJ198832.1|BJ198832
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTA
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTA
EST: gi|100397833|gb|BY990424.1|BY990424
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|162172938|gb|FC348943.1|FC348943
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|208359935|gb|DC938956.1|DC938956
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|162167595|gb|FC343740.1|FC343740
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|18358325|gb|BJ190384.1|BJ190384
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|18372637|gb|BJ204239.1|BJ204239
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|100373109|gb|BY949215.1|BY949215
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|162157447|gb|FC333211.1|FC333211
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|100383769|gb|BY969298.1|BY969298
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|100361559|gb|BY984067.1|BY984067
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|18327150|gb|BJ159151.1|BJ159151
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|208364270|gb|DC935541.1|DC935541
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|18362471|gb|BJ194541.1|BJ194541
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|100358066|gb|BY965455.1|BY965455
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
EST: gi|18329338|gb|BJ161344.1|BJ161344
EST:     GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAG                         TACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG
genomic: GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTG

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), 33 (downstream exon)
Score: 44

GCTGAGAAGAAAATGCTGGAAGGTGGCGACAACAAAGAGgtactttttc ... tggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTGCTATTGGGAGCCGACAACGCCGCCATTAAAGAGAACCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgattcactcagacctctaaaactggttctatgtaattcttgtggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTGCTATTGGGAGCCGACAACGCCGCCATTAAAGAGAACCGG
                 ctctaaa  putative branch site (score: 44)
                                       ttcttgt  putative PPT
                                tatgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttgcatgctttcttaatgctttcattttcttcttacgttagcggttgattcactcagacctctaaaactggttctatgtaattcttgtggtgtgcagTACCTTCCCATTGAGGGACTTGCTGCTTTCAACAAGGCTACTGCAGAGTTGCTATTGGGAGCCGACAACGCCGCCATTAAAGAGAACCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA