Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgcggatgtcatcgtttccttcgtttctgcaaccttaatgtattttatgctctcttttattgaggtattttctaaattactcaactattgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCAGCCGCTAGGGCAGAAGAATTGCGACTTCAACAAGAG

Basic information

species Physcomitrella patens
transcript PP1S32_313V6.1
intron # 5
splice site 3'
intron type U2

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|162156032|gb|FC332199.1|FC332199
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|67693131|gb|BJ953364.1|BJ953364
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162169716|gb|FC345253.1|FC345253
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162169717|gb|FC345254.1|FC345254
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162172209|gb|FC348774.1|FC348774
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|208396322|gb|DC920030.1|DC920030
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162249173|gb|FC420398.1|FC420398
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162252958|gb|FC429019.1|FC429019
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|208365127|gb|DC947335.1|DC947335
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162158826|gb|FC335349.1|FC335349
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162211540|gb|FC387620.1|FC387620
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162196282|gb|FC375391.1|FC375391
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|208396404|gb|DC920070.1|DC920070
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162223594|gb|FC399718.1|FC399718
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162188261|gb|FC364755.1|FC364755
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162188260|gb|FC364754.1|FC364754
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162196281|gb|FC375390.1|FC375390
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|208387159|gb|DC945458.1|DC945458
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162263938|gb|FC439207.1|FC439207
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162223593|gb|FC399717.1|FC399717
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|18341631|gb|BJ173666.1|BJ173666
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|208392949|gb|DC928635.1|DC928635
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162249172|gb|FC420397.1|FC420397
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|67725166|gb|BJ975425.1|BJ975425
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|208389104|gb|DC945680.1|DC945680
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|67722759|gb|BJ973018.1|BJ973018
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162187439|gb|FC362661.1|FC362661
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162244466|gb|FC422639.1|FC422639
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
EST: gi|162222297|gb|FC397109.1|FC397109
EST:     AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAG                         GCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA
genomic: AGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCA

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: 30

GAGTCAGGATAAGGACAGAGGCCGTATTAGTTTGTCCACCAAGAAGCTTGAGCCAACACCTGGTGACATGTTGCGCAATCCACAATTGGTTTATGAGAAGgtaagttttt ... tgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCAGCCGCTAGGGCAGAAGAATTGCGACTTCAACAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgctctcttttattgaggtattttctaaattactcaactattgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCAGCCGCTAGGGCAGAAGAATTGCGACTTCAACAAGAG
                          ttctaaa  putative branch site (score: 30)
                                            ttgcccc  putative PPT
                      tattttctaaattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgcggatgtcatcgtttccttcgtttctgcaaccttaatgtattttatgctctcttttattgaggtattttctaaattactcaactattgccccatagGCTGACGAGATGGCCAAGACATTTAGGCAAAGAGTTGCCCAAGCCGAGGCAGCCGCTAGGGCAGAAGAATTGCGACTTCAACAAGAG

- - - - - - - - - - - - - ttctgca