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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttcgaacatatccttttcaactatgtgataagctatctacgtcaattttctggacatctaacgttaaattcttaaaaactgctacctgatggtgttttactcctttctcttgagctggatacatgtatatgaagtcgtgactaaataattataacccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCAAAGAAGCCAACTGATAAATACATTCAGGTGGTGACGACAGATGGACATG

Basic information

species Physcomitrella patens
transcript PP1S78_27V6.1
intron # 4
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|162258232|gb|FC434631.1|FC434631
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|162271808|gb|FC448941.1|FC448941
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|162251814|gb|FC427546.1|FC427546
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|37842263|gb|BJ600271.1|BJ600271
EST:     TTGACGTACTATCCCCACCCCTGGCCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: TTGACGTACTAT-CCCACCCCTGG-CCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|162242692|gb|FC416383.1|FC416383
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208374673|gb|DC948645.1|DC948645
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208382718|gb|DC928479.1|DC928479
EST:     CTCCAGTTA-TAC-AN                         GNTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGNTGCGAACGCA
genomic: CTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|162258231|gb|FC434630.1|FC434630
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|100392454|gb|BY953371.1|BY953371
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|67694428|gb|BJ954661.1|BJ954661
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208385225|gb|DC923591.1|DC923591
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGACGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208355239|gb|DC949789.1|DC949789
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|162271809|gb|FC448942.1|FC448942
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208374197|gb|DC945243.1|DC945243
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208353654|gb|DC922128.1|DC922128
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208384413|gb|DC928164.1|DC928164
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208362981|gb|DC946892.1|DC946892
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|37828136|gb|BJ586148.1|BJ586148
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|37825984|gb|BJ584050.1|BJ584050
EST:     GGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: GGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208352534|gb|DC918243.1|DC918243
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTANCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|162272036|gb|FC448454.1|FC448454
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208381635|gb|DC915501.1|DC915501
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208346585|gb|DC916851.1|DC916851
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|37852720|gb|BJ610728.1|BJ610728
EST:     CCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: CCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208350120|gb|DC921487.1|DC921487
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|37835053|gb|BJ593065.1|BJ593065
EST:     CTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: CTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|37844181|gb|BJ602189.1|BJ602189
EST:     CCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: CCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|67726088|gb|BJ976347.1|BJ976347
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208384438|gb|DC928189.1|DC928189
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|18338051|gb|BJ170075.1|BJ170075
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|37828148|gb|BJ586160.1|BJ586160
EST:     TTGACGTACTATCCCCACCCCTGGCCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: TTGACGTACTAT-CCCACCCCTGG-CCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|100442322|gb|BY981346.1|BY981346
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGGTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|37828990|gb|BJ587002.1|BJ587002
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|208372211|gb|DC948014.1|DC948014
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
EST: gi|100373686|gb|BY967780.1|BY967780
EST:     AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAG                         GTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA
genomic: AGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCA

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), 22 (downstream exon)
Score: 2

TGGCACGCTGTATATCACCAATAAAAAGTTTGCCTTCTGCAGTGACCGGGAGTTGACGTACTATCCCACCCCTGGCCAGGCGGCCTCCAGTTATTACAAGgtaccttcga ... ccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCAAAGAAGCCAACTGATAAATACATTCAGGTGGTGACGACAGATGGACATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagctggatacatgtatatgaagtcgtgactaaataattataacccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCAAAGAAGCCAACTGATAAATACATTCAGGTGGTGACGACAGATGGACATG
                                      ttataac  putative branch site (score: 2)
                                            cccatcc  CT-rich tract
                           tgactaaataattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccttcgaacatatccttttcaactatgtgataagctatctacgtcaattttctggacatctaacgttaaattcttaaaaactgctacctgatggtgttttactcctttctcttgagctggatacatgtatatgaagtcgtgactaaataattataacccatccgcagGTTATCGTACCATTAGAGAATGTAAGGGAGGTTATATCAGTTGCGAACGCAAAGAAGCCAACTGATAAATACATTCAGGTGGTGACGACAGATGGACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA