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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattacatgtttggtgtttgaatgtggtggatagcatcctttgcttgtatgaaatgctacgatttcttttgtggtactgatatgatgcgaagaggcgatgctgataattttttctgcaattttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAGAATGAGATGCTTGCTTTCTCTCCAGGAGTGGTGCCCCCTGGAATCACTT

Basic information

species Physcomitrella patens
transcript PP1S259_126V6.1
intron # 6
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|208362855|gb|DC950805.1|DC950805
EST:     CCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTNGGATAACTTCTTCAGCGA
genomic: CCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTT-GGATAACTTCTTCAGCGA
EST: gi|208375077|gb|DC956445.1|DC956445
EST:     AATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: AATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208363794|gb|DC943251.1|DC943251
EST:     ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208392829|gb|DC957096.1|DC957096
EST:     CCCAATGGACACTACNTGCATNTGGNCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGA
genomic: CCCAATGGACACTACCTGCATCTGG-CCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGT-GGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGA
EST: gi|208360610|gb|DC957849.1|DC957849
EST:     ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208388440|gb|DC957050.1|DC957050
EST:     CAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: CAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208369501|gb|DC931697.1|DC931697
EST:     ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208394053|gb|DC957134.1|DC957134
EST:     GGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATTGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: GGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208361228|gb|DC957697.1|DC957697
EST:     ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208386921|gb|DC956918.1|DC956918
EST:     ACCCAATGGACANTACNTGCATCTGGCCGGAGGAGTTGTTTCCTNTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208394129|gb|DC957210.1|DC957210
EST:     CCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: CCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208389271|gb|DC933299.1|DC933299
EST:     ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAATAAGAATTTGGATAACTTCTTCAGCGAG
genomic: ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
EST: gi|208377437|gb|DC927083.1|DC927083
EST:     ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAG                         CCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG
genomic: ACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAG

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: 32

GCTGTATATCCAGACAATGAACCCTAGCGACGAAGACAAGTACGACTTCGACCCAATGGACACTACCTGCATCTGGCCGGAGGAGTTGTTTCCTCTGCAGgtaagattac ... ttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAGAATGAGATGCTTGCTTTCTCTCCAGGAGTGGTGCCCCCTGGAATCACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatatgatgcgaagaggcgatgctgataattttttctgcaattttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAGAATGAGATGCTTGCTTTCTCTCCAGGAGTGGTGCCCCCTGGAATCACTT
                         tgataattttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattacatgtttggtgtttgaatgtggtggatagcatcctttgcttgtatgaaatgctacgatttcttttgtggtactgatatgatgcgaagaggcgatgctgataattttttctgcaattttgagtgcagCCGGTGGGACGTATGGTGTTGAACAAGAATTTGGATAACTTCTTCAGCGAGAATGAGATGCTTGCTTTCTCTCCAGGAGTGGTGCCCCCTGGAATCACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG