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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactgtacttgtattctcatcctagggcaactttttgattatggaaagttaggaaaggtctcatgcatgacataatgaattcaagccttcaccttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGATGACGGTATTCGGCCTGGGACATCCCTTGCTGACTTGTCGAAGTTGAAGA

Basic information

species Physcomitrella patens
transcript PP1S67_59V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S67_59V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 8
aactgtacttgtattctcatcctagggcaactttttgattatggaaagttaggaaaggtctc----atgcatgacataatgaattc---aagccttcac-cttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGATGACGGTATTCGGCCTGGGACATCCCTTGCTGACTTGTCGAAGTTGAAGA
       |||||  ||| | |  |    | |  | || |||   |     || | || |||     ||| || |  |   |  ||    ||  || ||   |   ||||| ||||||||||||||||||||||||||| |||| || || || |  ||||| || ||| |||| |||||  |     |||  ||| ||||  ||||  
------gcttgttgtctgacc--aaattatcaatctggttacctaggaacagaagagttctttgatatgtattatttcgagcgtttgctaacactccatattctgcagATCGTTGATCCTAAAACTGGAGAGGAGAAGGAAGTTGTGATATCAGTTGATGATGGGATTAGGCCAGGGACCACAGCATCTGGATTGGCGAAACTGAAAC
















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|18372877|gb|BJ204479.1|BJ204479
EST:     CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAG                         ATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGAT
genomic: CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAGgtattttgtg ... accttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGAT
EST: gi|162187341|gb|FC363499.1|FC363499
EST:     CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAG                         ATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGAT
genomic: CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAGgtattttgtg ... accttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGAT
EST: gi|162213624|gb|FC389704.1|FC389704
EST:     CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAG                         ATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGAT
genomic: CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAGgtattttgtg ... accttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGAT
EST: gi|100403518|gb|BY954966.1|BY954966
EST:     CCAGGGCTTCTGGCAGAT-CAAAGATGAAATAATTCCTGTGCACACCAAG                         ATTGTTGATCCTAAA-CTGGAGA
genomic: CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAGgtattttgtg ... accttgacagATTGTTGATCCTAAAACTGGAGA
EST: gi|162184204|gb|FC360471.1|FC360471
EST:     CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAG                         ATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGAT
genomic: CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAGgtattttgtg ... accttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGAT
EST: gi|100362596|gb|BY947432.1|BY947432
EST:     AGGGCTTCTGGGGCAGAT-CAA-GATGAAATAATTCCTGTGCACACCANG                         ATTTGT-GATCCCTAAA-CTGGA
genomic: AGGGCTTCTGG--CAGATTCAAAGATGAAATAATTCCTGTGCACACCAAGgtattttgtg ... accttgacagATT-GTTGATCC-TAAAACTGGA
EST: gi|162264638|gb|FC441636.1|FC441636
EST:     CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAG                         ATTGTTGATCCTAAAACTGGAGAGGAGAAGNCA-GTAGTCATCTCCGAGGA
genomic: CCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAGgtattttgtg ... accttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAG-CAAGTAGTCATCTCCGAGGA

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: 31 (upstream exon), 33 (downstream exon)
Score: 32

GTCAAATCGCATGCAAAGGCGGCAGCTGCCAGGGCTTCTGGCAGATTCAAAGATGAAATAATTCCTGTGCACACCAAGgtattttgtg ... accttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGATGACGGTATTCGGCCTGGGACATCCCTTGCTGACTTGTCGAAGTTGAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagttaggaaaggtctcatgcatgacataatgaattcaagccttcaccttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGATGACGGTATTCGGCCTGGGACATCCCTTGCTGACTTGTCGAAGTTGAAGA
                                        ccttcacctt  CT-rich tract
                          ataatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactgtacttgtattctcatcctagggcaactttttgattatggaaagttaggaaaggtctcatgcatgacataatgaattcaagccttcaccttgacagATTGTTGATCCTAAAACTGGAGAGGAGAAGCAAGTAGTCATCTCCGAGGATGACGGTATTCGGCCTGGGACATCCCTTGCTGACTTGTCGAAGTTGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcatgc