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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgtgagccgacttcgaatcgttcaatgtggatttgtttggttgtggctcaactaccggagtgtgtcacagtcctgtttgcaaacaaataattgtttattgttttctttttcgctttcctttaccgggacgatgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTCCCATGGGTGGGAAGTATCAACAAATTAGAGAACAGCAAGAACTACGCCA

Basic information

species Physcomitrella patens
transcript PP1S419_7V6.1
intron # 5
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|162194293|gb|FC369516.1|FC369516
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162256614|gb|FC432924.1|FC432924
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162158128|gb|FC333923.1|FC333923
EST:     AATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: AATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162249202|gb|FC421545.1|FC421545
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162270721|gb|FC446334.1|FC446334
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162178773|gb|FC354510.1|FC354510
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162164877|gb|FC341366.1|FC341366
EST:     CTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: CTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162180667|gb|FC357024.1|FC357024
EST:     GGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: GGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162256588|gb|FC432898.1|FC432898
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|67701793|gb|BJ962026.1|BJ962026
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162256626|gb|FC432936.1|FC432936
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAN                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162165033|gb|FC342224.1|FC342224
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162188009|gb|FC364999.1|FC364999
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162173204|gb|FC349986.1|FC349986
EST:     CACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: CACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162240726|gb|FC416318.1|FC416318
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162245537|gb|FC423272.1|FC423272
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|100388490|gb|BY952092.1|BY952092
EST:     TGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|100386918|gb|BY988187.1|BY988187
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162154367|gb|FC330706.1|FC330706
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162167824|gb|FC344554.1|FC344554
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162200069|gb|FC376531.1|FC376531
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
EST: gi|162168254|gb|FC344984.1|FC344984
EST:     TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAG                         GCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC
genomic: TCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTC

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: 33 (upstream exon), 35 (downstream exon)
Score: 55

TATCAAGAGCAAACTCGATCCTGCGGAATTTGGTGATCCCACCTCTGCCATCACTGAGCAACACATTGACGCCAAATTGGAAGGTCTCAGCGTCGCGCAGgtaccgtgag ... atgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTCCCATGGGTGGGAAGTATCAACAAATTAGAGAACAGCAAGAACTACGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataattgtttattgttttctttttcgctttcctttaccgggacgatgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTCCCATGGGTGGGAAGTATCAACAAATTAGAGAACAGCAAGAACTACGCCA
        tttattgttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccgtgagccgacttcgaatcgttcaatgtggatttgtttggttgtggctcaactaccggagtgtgtcacagtcctgtttgcaaacaaataattgtttattgttttctttttcgctttcctttaccgggacgatgcgcgcagGCCGTGTCCGAGAAGAAGCTTTTTGTGGTGGACTTTCACGATCTTTTTCTCCCATGGGTGGGAAGTATCAACAAATTAGAGAACAGCAAGAACTACGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC