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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctttttcgcagttgcaaaatgtgagtacaaggctggggattatgtgtacattgaactgcattgttcagacaattgatttctctctctgaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTGGAGTGGCTTGCGAAGAACAAATGAACATTTTCGCAAATTCCCATACCCG

Basic information

species Physcomitrella patens
transcript PP1S392_44V6.1
intron # 3
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|208349937|gb|DC913645.1|DC913645
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|162244334|gb|FC421012.1|FC421012
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|162264904|gb|FC440679.1|FC440679
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGANAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|37833776|gb|BJ591788.1|BJ591788
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|162214573|gb|FC391540.1|FC391540
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|162218325|gb|FC394499.1|FC394499
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|208380127|gb|DC927406.1|DC927406
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|162264903|gb|FC440678.1|FC440678
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|18356835|gb|BJ188894.1|BJ188894
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
EST: gi|100381545|gb|BY950122.1|BY950122
EST:     TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAG                         GGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG
genomic: TGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTG

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), 29 (downstream exon)
Score: 17

AGGCTGGAAGACTACTACCGGCGCAACTTCACAGAATACTTTCAGTTTGTGGAGgtaaaatcaa ... gaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTGGAGTGGCTTGCGAAGAACAAATGAACATTTTCGCAAATTCCCATACCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtacattgaactgcattgttcagacaattgatttctctctctgaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTGGAGTGGCTTGCGAAGAACAAATGAACATTTTCGCAAATTCCCATACCCG
                            aattgat  putative branch site (score: 17)
                                  tttctctctctg  CT-rich tract
                            aattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctttttcgcagttgcaaaatgtgagtacaaggctggggattatgtgtacattgaactgcattgttcagacaattgatttctctctctgaatttgcagGGTTCCGTGAGGAACAAGAAAGAGCTGACTCCGGCTGAAAAAGCTATTGTGGAGTGGCTTGCGAAGAACAAATGAACATTTTCGCAAATTCCCATACCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC