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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttttcttttttcttttttttgtttaatgttagctctgtttttattctagaccctttgaagtgttttgtatatttagtatgattacactcctatgtttttgggttccttggtatattgtaaaagagatctcacattttacttctatattgtcag

Basic information

species Physcomitrella patens
transcript PP1S215_25V6.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA04G41130.2 (Glycine max), 5'ss of exon 7
TAAGAGCA-TCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttttcttttttcttttttttgtttaatgttagctctgtttttattctagaccctttgaagtgttttgtatatttagtatgattacactcctatgtttttgggttccttggtatattgtaaaagagatctcacattttacttctatattgtcag
 || |||| |||| ||||||||||| || |||||| |||||||||||||||| || || ||||||||    ||  | | |    |  || ||||||     || | || ||   || | ||    |  | |||| |    ||||||       ||   ||   ||||        | | ||| |||                                       
-AAAAGCAATCAATAAGGGCATTGGGGTTGACAACTTGCATTATCTCAATGATGGTCTTTGGAAGgtatggttgatatatgcattccttcttgtttg----tatcactattaagatacaag--tatacgtagtgctc---atattt-------ttgttctttgatgt------agtacctggaataa--------------------------------------

upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT1G09150.1 (Arabidopsis thaliana), 5'ss of exon 8
TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttttcttttttcttttttttgtt--taatgttagctc-tgtttttattctagaccctttgaagtgttttgtatatttagtatgattacac-tcctatgtttttgggttccttggtatattgtaaaagagatctcacattttacttctatattgtcag
 |||||||| ||||| || || ||||| |||||||||||||| ||||| ||||| || |||||||| |   |  |  | | |  ||| | | ||  || | ||  |      | | ||| | ||   | | ||        |  |||| | | ||  |||  ||  | |||| ||   |      | ||||| |                                  
AAAGAGCATTAACAAAGGAATAGGAGTTGACAACATGCATTACCTCAACGACGGTCTCTGGAAGgtaccaatacttgtctctggtttctctattcgtagtattgccaagcagtctcattgttga---tataaaa------atcgattttggaagaacacaaatcaaaagtttctgaaatt-----tgtattgcag---------------------------------

upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv14s0060g01920.t01 (Vitis vinifera), 5'ss of exon 7
TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgct-ttttttcttttttcttttttttgtttaatgttagctctgtttttattctagaccctttgaagtgttttgtatatttagtatgattacactcctatgtttttgggttccttggtatattgtaaaagagatctcacattttacttctatattgtcag
||     |||||||| || ||||| ||||| ||||||||||| ||||||||||| || |||||||| ||  ||| |  ||   | ||  | | |||     |  |||  | |  |||| |   |   |    |  |||| |   ||   ||  ||| | ||  |   ||                                                        
TAGAGCAATCAACAAAGGAATTGGCGTGGATAACATGCATTACCTCAATGACGGGCTGTGGAAGgtactactttatacttaaaccttcatctcttt----cttcctccatatgcattcaatggctcattttattctttggaaggttctcattgttaaa-tctcagactt--------------------------------------------------------

upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EDP06185 (Chlamydomonas reinhardtii), 5'ss of exon 5
------------------------------------TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttttcttttttcttttttttgtttaatgttagctctgtttttattctagaccctttgaagtgttttgtatatttagtatgattacactcctatgtttttgggttccttggtatattgtaaaagagatctcacattttacttctatattgtcag
                                         || | ||||||||||| || ||||| ||||||||  | ||||| ||||| |||||||||||||       |            |  ||  |  |   |    | |||| |    ||     || ||||    |      | |   |       |  | ||     ||                                                    
GGCTGTGGGCGTGCTGCAGATGTCAACAGCCGACATCCGCGGCGTTAACAAGGGCATCGGCGTGGAGAACATGCACCACCTCAACGACGGCCTATGGAAGgtgcgggggggcggagggagagggtgcgtggagcgggcg----ggttttgt---ggagagggtggagtggagagggcgggtggagagggcggg-tggtgtggagaggg----------------------------------------------------

upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ21050 (Selaginella moellendorffii), 5'ss of exon 8
TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttttcttttttcttttttttgtttaatgttagctctgtttttattctagaccctttgaagtgttttgtatatttagtatgattacactcctatgtttttgggttccttggtatattgtaaaagagatctcacattttacttctatattgtcag
 ||||  |||||||| || |||||||||||||| ||||| |||||||| || ||||| ||||||||   |           |   |  |      ||    | || | |||  |                                                                                                              
AAAGAATATCAACAAAGGGATTGGAGTGGACAATATGCACTATCTCAACGATGGACTCTGGAAGgtatgtaacactaccaatggatgctaaccgaaaaaaaaactatctttccag-------------------------------------------------------------------------------------------------------------

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|208376363|gb|DC932273.1|DC932273
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|18356615|gb|BJ188674.1|BJ188674
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGG
EST: gi|208345629|gb|DC909299.1|DC909299
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|162259779|gb|FC436759.1|FC436759
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|208363408|gb|DC947006.1|DC947006
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|67700873|gb|BJ961106.1|BJ961106
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|22132705|gb|BQ827296.1|BQ827296
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|18341766|gb|BJ173801.1|BJ173801
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|208371667|gb|DC932496.1|DC932496
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|162259765|gb|FC436758.1|FC436758
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|162221749|gb|FC397081.1|FC397081
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGANATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|67578005|gb|BJ950172.1|BJ950172
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|37822681|gb|BJ580747.1|BJ580747
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|208365150|gb|DC946779.1|DC946779
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|37829219|gb|BJ587231.1|BJ587231
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|208354986|gb|DC914250.1|DC914250
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|162228094|gb|FC404649.1|FC404649
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|208382460|gb|DC927994.1|DC927994
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|7584206|gb|AW700103.1|AW700103
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|208395953|gb|DC915713.1|DC915713
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|18350245|gb|BJ182296.1|BJ182296
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGG
EST: gi|67693833|gb|BJ954066.1|BJ954066
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|208382492|gb|DC923162.1|DC923162
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|37836518|gb|BJ594526.1|BJ594526
EST:     TGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: TGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
EST: gi|162221748|gb|FC397080.1|FC397080
EST:     AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAG                         ACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG
genomic: AGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACG

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), 20 (downstream exon)
Score: 6

TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttt ... atattgtcagACGTTACATCTTGACTGAAATATGATGGAGACAACGTGTGACTTGGTAACGAGGCATTTCTGGGTTAGCTTTTCAAGATTGCTGGCGGTGCATACATGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGAGCATCAACAAGGGCATTGGAGTGGACAACATGCATTATCTCAATGACGGACTATGGAAGgtgctttttttcttttttcttttttttgtttaatgttagctctgtttttattctagaccctttgaagtgttttgtatatttagtatgattacactcctatgtttttgggttccttggtatattgtaaaagagatctcacattttacttctatattgtcag

- - - - - - - - - - TTGGAG
- - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG