Skip to another splice site:
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 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataccggttacccctgttccatttgctcggcgttgttatgatacatcatttaaaagtttgatggtcgttacggaattcggtattcagtaatctaactgtcgtaattttcttgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATTGAATCAATTTTCGTACCCTACTAACCACGTCGCCCTCTCTAGTGTCAAC

Basic information

species Physcomitrella patens
transcript PP1S99_129V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA01G35130.2 (Glycine max), 3'ss of exon 6
-------------------------------------gtaataccggttacccctgttccatttgctcggcgttgttatgatacatcatttaaaagtttgatggtcgttacggaattcggtattcagtaatctaactgtcgtaattttctt----------gttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATTGAATCAATTTTCGTACCCTACTAACCACGTCGCCCTCTCTAGTGTCAAC
                                     ||   |     |        | | || ||| |    | ||   |    |  || ||||   | ||  |  | |     |     |   | |  ||||||  |    ||||| ||          ||| | ||||||||   | ||||||||||||||||||| ||||| ||||||||| | || ||| | ||| ||  |   ||        |   ||  | ||      || 
gtaagtctcatattttcctttcactagtttattttgtgttgaaataactcaaataagtacgttggcttgtttctattcaaaactctttttaaaaacactaataatgttaataatttaaaccagctaattgtctaacattgcagattttttttgaaactattgttttgcagGAGTTCGGGCTGATTGACAAAAAGGAGCTGGCACCCCTTCAAGAGCTTATAGAAACCATTATCCCATATTAAATGAATTGGGACCTACCCTCTGAAAAAT
















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|162170893|gb|FC346584.1|FC346584
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|67695206|gb|BJ955439.1|BJ955439
EST:     AGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|37841636|gb|BJ599644.1|BJ599644
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162246776|gb|FC423874.1|FC423874
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162230785|gb|FC406416.1|FC406416
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162240619|gb|FC419162.1|FC419162
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|67697574|gb|BJ957807.1|BJ957807
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162215256|gb|FC391648.1|FC391648
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|7584173|gb|AW700071.1|AW700071
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCG
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCG
EST: gi|162170894|gb|FC346585.1|FC346585
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162266887|gb|FC443001.1|FC443001
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|67726815|gb|BJ977074.1|BJ977074
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162216807|gb|FC392183.1|FC392183
EST:     CAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: CAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|37844367|gb|BJ602375.1|BJ602375
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162230786|gb|FC406417.1|FC406417
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162240620|gb|FC419163.1|FC419163
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|67694230|gb|BJ954463.1|BJ954463
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162215557|gb|FC391649.1|FC391649
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|7207622|gb|AW561562.1|AW561562
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTGTATCCTTTTCACTCAT                         GAGTTGTCGTTGATTGACAAAAAGGAGCTC
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTC
EST: gi|67694212|gb|BJ954445.1|BJ954445
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|37845448|gb|BJ603456.1|BJ603456
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162266886|gb|FC443000.1|FC443000
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|67699369|gb|BJ959602.1|BJ959602
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|67693080|gb|BJ953313.1|BJ953313
EST:     AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
EST: gi|162246775|gb|FC423873.1|FC423873
EST:     AAGAGGCCCATTTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCAT                         GAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT
genomic: AAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATT

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), 33 (downstream exon)
Score: 3

TTATGCACATATATACCACTCTCACTTTCAGAAGATTGTCAGTCTCAAAGAAGAGGCCCATCTGAACACCTGCTTCAAGCACTTTATCCTTTTCACTCATgtaataccgg ... tgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATTGAATCAATTTTCGTACCCTACTAACCACGTCGCCCTCTCTAGTGTCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttacggaattcggtattcagtaatctaactgtcgtaattttcttgttattcagGAGTTTTCGTTGATTGACAAAAAGGAGCTCGCACCACTTCAAGAGTTGATTGAATCAATTTTCGTACCCTACTAACCACGTCGCCCTCTCTAGTGTCAAC
                        atctaac  putative branch site (score: 3)
                                       ttttcttgttattc  putative PPT
                                    taattttcttgttatt  TA-rich tract