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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaatgtatgagtgaaatctgtgtccgttgctcttattatcattgaataactgtgtgcttgttgaccttatgttgaagtttcattctattttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTGAAGCAAAGATCGAATGTCGTGGCTGTGACTGGTGATGGAACTAACGACG

Basic information

species Physcomitrella patens
transcript PP1S8_288V6.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 25
tgtgaatgtatgagtgaaatctgtgtccgttgctcttattatcattgaataactgtgtgcttgttgaccttatgttgaagtttcattctattttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTGAAGCAAAGATCGAATGTCGTGGCTGTGACTGGTGATGGAACTAACGACG
             || | | |  | |       | |  || | | |||  |||  | |        |||| |  |||  | |  | |  |        ||||||||| ||| || || || | ||| || ||    || ||| |  |  |||||   ||     | |||||||||||||||||||||||||| || || |
-------------gtaagagccttatg----attttggttgtgactgaggaacattatttaatggtacctgacattgttgctaaacttga--------agGTAATGGGTAGATCATCACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATG
















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|162166640|gb|FC343532.1|FC343532
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTG
EST: gi|162259197|gb|FC435217.1|FC435217
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|162180511|gb|FC356153.1|FC356153
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|162153113|gb|FC329519.1|FC329519
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|162155067|gb|FC330861.1|FC330861
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|100367439|gb|BY984706.1|BY984706
EST:     AGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: AGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|162208804|gb|FC384940.1|FC384940
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|162191836|gb|FC367985.1|FC367985
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|162175273|gb|FC351471.1|FC351471
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|100413350|gb|BY956628.1|BY956628
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|100443051|gb|BY981677.1|BY981677
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|162181321|gb|FC358416.1|FC358416
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
EST: gi|162205305|gb|FC380987.1|FC380987
EST:     TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTA                         GTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG
genomic: TTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTG

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: 79

AGAATGTGGTATTCTCACAGAAGGTGGTCTTGTAGTCGAGGGACCTGATTTTAGAACATGGGATGAAGCGCGCATCGATAGAGATATTGAAAAGCTTGTAgtaaggattc ... ttttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTGAAGCAAAGATCGAATGTCGTGGCTGTGACTGGTGATGGAACTAACGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaataactgtgtgcttgttgaccttatgttgaagtttcattctattttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTGAAGCAAAGATCGAATGTCGTGGCTGTGACTGGTGATGGAACTAACGACG
                                   tttcattctattttct  CT-rich tract
                                   tttcattctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaatgtatgagtgaaatctgtgtccgttgctcttattatcattgaataactgtgtgcttgttgaccttatgttgaagtttcattctattttctccagGTAATGGCTAGGTCGTCTCCTACTGATAAGCTCAAGCTGGTGAAGGCATTGAAGCAAAGATCGAATGTCGTGGCTGTGACTGGTGATGGAACTAACGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgaa