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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcattgtgtatgccttgcttggttgaggggcggtcgtatcaacttttggaacttatgttcttctgttgacactgataagttcttttgttggaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAGGCCCGTGTTAGCGGTGCAGATGCTGTCCTCTTAATAGCAGCAGTGCTGC

Basic information

species Physcomitrella patens
transcript PP1S330_9V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S330_9V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G42680.1 (Glycine max), 3'ss of exon 5
tcattgtgtatgccttgcttggttgaggggcggtcgtatcaacttttggaacttatgttcttctgttgacactgataagttcttttgttggaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAGGCCCGTGTTAGCGGTGCAGATGCTGTCCTCTTAATAGCAGCAGTGCTGC
   |  | ||||  |||| | ||    |     | | ||  | | |   |  | |||  ||| ||| |||  || | |   || | |    ||| |  |||||||  | |||||||||||||||||||| ||||| |||||| ||||| | || ||   ||  ||||||||||| ||||| ||||| || || ||  |||
gtttgttttatgaattgcatagtccctgat--attggatttattataccatttaatgc-cttttgtagaccatgttgatgactctggacaaaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC

upper sequence: PP1S330_9V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G05810.2 (Glycine max), 3'ss of exon 5
tcattgtgtatgccttgcttggttgaggggcggtcgtatcaacttttggaacttatgttcttctgttgacactgataagttcttttgttggaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAGGCCCGTGTTAGCGGTGCAGATGCTGTCCTCTTAATAGCAGCAGTGCTGC
                            |   ||  | | || ||    |     || | ||   || |   |   |     | || || |||| |  |||||||  | |||||||||||||||||||| ||||| |||||| ||||| | || ||   ||  ||||||||||| ||||| ||||| || || ||  |||
----------------------------gtttgttttgtgaa-ttgcatagtccctgatattggatttattataccatcaaatgttttttgaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC
















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|162176427|gb|FC353820.1|FC353820
EST:     TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
EST: gi|208395485|gb|DC924511.1|DC924511
EST:     TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
EST: gi|208392835|gb|DC957102.1|DC957102
EST:     TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
EST: gi|162204346|gb|FC380534.1|FC380534
EST:     TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
EST: gi|37838779|gb|BJ596787.1|BJ596787
EST:     TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
EST: gi|162228922|gb|FC404715.1|FC404715
EST:     AACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: AACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
EST: gi|162187994|gb|FC364984.1|FC364984
EST:     TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: TCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
EST: gi|162228923|gb|FC404716.1|FC404716
EST:     GAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAA
genomic: GAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCG-CTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAA
EST: gi|162150328|gb|FC326600.1|FC326600
EST:     TTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGC-TTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: TTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
EST: gi|37825505|gb|BJ583571.1|BJ583571
EST:     CCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAA                         TGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG
genomic: CCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAG

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: 29 (upstream exon), 28 (downstream exon)
Score: 12

TGAAAAGGGTGGAGCTACTTGTTTGAGTGTATTGACGGATTCCAAATATTTCCAAGGAGGATTTGAGAACTTGAGACTAATCAGGAATGCTGGGGTCCAAgtacgttagt ... gaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAGGCCCGTGTTAGCGGTGCAGATGCTGTCCTCTTAATAGCAGCAGTGCTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaacttatgttcttctgttgacactgataagttcttttgttggaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAGGCCCGTGTTAGCGGTGCAGATGCTGTCCTCTTAATAGCAGCAGTGCTGC
                        cactgat  putative branch site (score: 12)
                                                tttct  putative PPT
                                              aatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcattgtgtatgccttgcttggttgaggggcggtcgtatcaacttttggaacttatgttcttctgttgacactgataagttcttttgttggaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAGGCCCGTGTTAGCGGTGCAGATGCTGTCCTCTTAATAGCAGCAGTGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC